INFO 09:09:28,004 QScriptManager - Compiling 2 QScripts INFO 09:09:32,883 QScriptManager - Compilation complete INFO 09:09:32,950 HelpFormatter - ---------------------------------------------------------------------- INFO 09:09:32,950 HelpFormatter - Queue v3.7.GS-r1748-0-g74bfe0b, Compiled 2017/10/06 08:08:49 INFO 09:09:32,950 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 09:09:32,951 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 09:09:32,951 HelpFormatter - Program Args: -S /work/SoftW/svtoolkit/qscript/SVPreprocess.q -S /work/SoftW/svtoolkit/qscript/SVQScript.q -gatk /work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar --disableJobReport -cp /work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_parameters.txt -tempDir IEMS/tmpdir_SVPreprocess -R /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta -genomeMaskFile /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta -copyNumberMaskFile /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta -genderMapFile IEMS_gender.map -runDirectory IEMS -md IEMS/metadata -disableGATKTraversal -useMultiStep -reduceInsertSizeDistributions false -computeGCProfiles true -computeReadCounts true -jobLogDir IEMS/logs -I IEMS.list -run INFO 09:09:32,951 HelpFormatter - Executing as wsh@localhost on Linux 2.6.32-696.6.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_141-b15. INFO 09:09:32,952 HelpFormatter - Date/Time: 2018/02/01 09:09:32 INFO 09:09:32,952 HelpFormatter - ---------------------------------------------------------------------- INFO 09:09:32,952 HelpFormatter - ---------------------------------------------------------------------- INFO 09:09:32,957 QCommandLine - Scripting SVPreprocess 1:1-10000000 1:10000001-20000000 1:20000001-30000000 1:30000001-40000000 1:40000001-50000000 1:50000001-60000000 1:60000001-70000000 1:70000001-80000000 1:80000001-90000000 1:90000001-100000000 1:100000001-110000000 1:110000001-120000000 1:120000001-130000000 1:130000001-140000000 1:140000001-150000000 1:150000001-160000000 1:160000001-170000000 1:170000001-180000000 1:180000001-190000000 1:190000001-200000000 1:200000001-210000000 1:210000001-220000000 1:220000001-230000000 1:230000001-240000000 1:240000001-249250621 2:1-10000000 2:10000001-20000000 2:20000001-30000000 2:30000001-40000000 2:40000001-50000000 2:50000001-60000000 2:60000001-70000000 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GL000192.1:1-547496 GL000225.1:1-211173 GL000194.1:1-191469 GL000193.1:1-189789 GL000200.1:1-187035 GL000222.1:1-186861 GL000212.1:1-186858 GL000195.1:1-182896 GL000223.1:1-180455 GL000224.1:1-179693 GL000219.1:1-179198 GL000205.1:1-174588 GL000215.1:1-172545 GL000216.1:1-172294 GL000217.1:1-172149 NC_007605:1-171823 GL000199.1:1-169874 GL000211.1:1-166566 GL000213.1:1-164239 GL000220.1:1-161802 GL000218.1:1-161147 GL000209.1:1-159169 GL000221.1:1-155397 GL000214.1:1-137718 GL000228.1:1-129120 GL000227.1:1-128374 GL000191.1:1-106433 GL000208.1:1-92689 GL000198.1:1-90085 GL000204.1:1-81310 GL000233.1:1-45941 GL000237.1:1-45867 GL000230.1:1-43691 GL000242.1:1-43523 GL000243.1:1-43341 GL000241.1:1-42152 GL000236.1:1-41934 GL000240.1:1-41933 GL000206.1:1-41001 GL000232.1:1-40652 GL000234.1:1-40531 GL000202.1:1-40103 GL000238.1:1-39939 GL000244.1:1-39929 GL000248.1:1-39786 GL000196.1:1-38914 GL000249.1:1-38502 GL000246.1:1-38154 GL000203.1:1-37498 GL000197.1:1-37175 GL000245.1:1-36651 GL000247.1:1-36422 GL000201.1:1-36148 GL000235.1:1-34474 GL000239.1:1-33824 GL000210.1:1-27682 GL000231.1:1-27386 GL000229.1:1-19913 MT:1-16569 GL000226.1:1-15008 GL000207.1:1-4262 INFO 09:09:33,402 QCommandLine - Added 933 functions INFO 09:09:33,402 QGraph - Generating graph. INFO 09:09:33,473 QGraph - Running jobs. INFO 09:09:33,577 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateMetaDataDirectory' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' INFO 09:09:33,578 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-1.out INFO 09:09:37,433 FunctionEdge - Starting: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ExtractBAMSubset' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/headers.bam' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-L' 'NONE' INFO 09:09:37,433 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-3.out INFO 09:09:41,326 QGraph - 931 Pend, 2 Run, 0 Fail, 0 Done INFO 09:10:03,573 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateMetaDataDirectory' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' INFO 09:10:03,574 FunctionEdge - Done: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ExtractBAMSubset' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/headers.bam' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-L' 'NONE' INFO 09:10:03,574 QGraph - Writing incremental jobs reports... INFO 09:10:03,588 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.SVToolkitInfo' INFO 09:10:03,589 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/svtoolkit.version.dat INFO 09:10:03,674 FunctionEdge - Starting: samtools index IEMS/metadata/headers.bam INFO 09:10:03,674 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-4.out INFO 09:10:03,680 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/genome_sizes.txt' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' INFO 09:10:03,680 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-5.out INFO 09:11:45,648 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/reference.gcprof.zip' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-md' 'IEMS/metadata' '-writeReferenceProfile' 'true' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-configFile' 'conf/genstrip_parameters.txt' INFO 09:11:45,649 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-6.out INFO 09:16:50,475 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120044-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120044-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/2017120044-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:16:50,475 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-7.out INFO 09:17:00,072 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120057-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120057-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/2017120057-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:17:00,072 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-8.out INFO 09:17:10,709 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120074-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120074-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/2017120074-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:17:10,709 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-9.out INFO 09:17:21,010 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120079-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120079-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/2017120079-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:17:21,010 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-10.out INFO 09:17:31,426 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120090-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120090-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/2017120090-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:17:31,426 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-11.out INFO 09:17:41,300 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK2CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK2CK4-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CK2CK4-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:17:41,300 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-12.out INFO 09:17:51,282 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK3-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK3-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CK3-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:17:51,282 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-13.out INFO 09:18:01,176 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK4-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CK4-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:18:01,176 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-14.out INFO 09:18:11,943 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK5-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK5-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CK5-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:18:11,943 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-15.out INFO 09:18:23,279 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120087-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120087-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120087-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:18:23,279 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-16.out INFO 09:18:32,649 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120089-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120089-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120089-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:18:32,650 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-17.out INFO 09:18:42,066 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120092-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120092-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120092-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:18:42,066 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-18.out INFO 09:18:52,418 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120093-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120093-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120093-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:18:52,418 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-19.out INFO 09:19:02,172 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120098-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120098-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120098-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:19:02,172 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-20.out INFO 09:19:11,948 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120106-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120106-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120106-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:19:11,953 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-21.out INFO 09:19:22,937 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120108-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120108-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120108-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:19:22,937 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-22.out INFO 09:19:33,529 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120111-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120111-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120111-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:19:33,529 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-23.out INFO 09:19:44,009 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120114-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120114-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120114-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:19:44,009 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-24.out INFO 09:19:54,056 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120115-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120115-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120115-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:19:54,056 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-25.out INFO 09:20:03,868 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120120-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120120-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120120-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:03,868 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-26.out INFO 09:20:13,718 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120121-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120121-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120121-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:13,718 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-27.out INFO 09:20:24,052 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120122-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120122-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120122-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:24,053 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-28.out INFO 09:20:33,586 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120123-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120123-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120123-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:33,586 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-29.out INFO 09:20:43,838 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120132-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120132-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120132-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:43,838 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-30.out INFO 09:20:53,441 QGraph - 903 Pend, 28 Run, 0 Fail, 2 Done ERROR 09:20:53,444 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.SVToolkitInfo' ERROR 09:20:53,445 FunctionEdge - Contents of /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/svtoolkit.version.dat: SVToolkit version 2.00 (build 1774) Build date: 2017/10/06 12:56:31 Web site: http://www.broadinstitute.org/software/genomestrip INFO 09:20:53,446 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/genome_sizes.txt' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' INFO 09:20:53,447 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120122-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120122-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120122-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,447 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120079-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120079-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/2017120079-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,448 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120111-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120111-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120111-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,448 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120090-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120090-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/2017120090-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,448 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK5-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK5-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CK5-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,449 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK4-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CK4-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,450 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120114-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120114-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120114-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,450 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120044-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120044-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/2017120044-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,450 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120093-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120093-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120093-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,451 FunctionEdge - Done: samtools index IEMS/metadata/headers.bam INFO 09:20:53,451 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120121-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120121-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120121-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,451 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120092-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120092-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120092-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,452 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120098-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120098-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120098-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,452 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120057-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120057-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/2017120057-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,453 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120132-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120132-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120132-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,453 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK3-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK3-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CK3-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,454 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120115-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120115-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120115-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,455 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120106-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120106-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120106-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,455 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120089-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120089-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120089-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,456 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/reference.gcprof.zip' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-md' 'IEMS/metadata' '-writeReferenceProfile' 'true' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-configFile' 'conf/genstrip_parameters.txt' INFO 09:20:53,456 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120123-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120123-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120123-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,457 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120120-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120120-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120120-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,458 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK2CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK2CK4-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CK2CK4-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,458 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120074-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120074-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/2017120074-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,459 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120108-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120108-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120108-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,459 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120087-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120087-IEMS.dedupped.hist.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-chimerismFile' 'IEMS/metadata/isd/CX2017120087-IEMS.dedupped.chimer.dat' '-createHistogramFile' 'true' -createEmpty INFO 09:20:53,460 QGraph - Writing incremental jobs reports... INFO 09:20:53,469 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeInsertSizeHistograms' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120044-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120057-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120074-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120079-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120090-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK2CK4-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK3-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK4-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK5-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120087-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120089-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120092-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120093-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120098-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120106-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120108-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120111-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120114-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120115-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120120-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120121-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120122-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120123-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120132-IEMS.dedupped.hist.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd.hist.bin' INFO 09:20:53,469 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-31.out INFO 09:20:57,231 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeChimerismFiles' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120044-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120057-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120074-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120079-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120090-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK2CK4-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK3-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK4-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK5-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120087-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120089-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120092-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120093-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120098-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120106-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120108-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120111-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120114-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120115-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120120-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120121-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120122-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120123-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120132-IEMS.dedupped.chimer.dat' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/chimerism.dat' INFO 09:20:57,232 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-33.out INFO 09:21:00,925 QGraph - 901 Pend, 2 Run, 1 Fail, 29 Done INFO 09:21:23,468 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeInsertSizeHistograms' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120044-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120057-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120074-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120079-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120090-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK2CK4-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK3-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK4-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK5-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120087-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120089-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120092-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120093-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120098-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120106-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120108-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120111-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120114-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120115-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120120-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120121-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120122-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120123-IEMS.dedupped.hist.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120132-IEMS.dedupped.hist.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd.hist.bin' INFO 09:21:23,469 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeChimerismFiles' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120044-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120057-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120074-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120079-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/2017120090-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK2CK4-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK3-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK4-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CK5-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120087-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120089-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120092-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120093-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120098-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120106-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120108-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120111-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120114-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120115-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120120-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120121-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120122-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120123-IEMS.dedupped.chimer.dat' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd/CX2017120132-IEMS.dedupped.chimer.dat' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/chimerism.dat' INFO 09:21:23,469 QGraph - Writing incremental jobs reports... INFO 09:21:23,477 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeInsertStatistics' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd.hist.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd.stats.dat' INFO 09:21:23,477 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-32.out INFO 09:21:27,312 QGraph - 900 Pend, 1 Run, 1 Fail, 31 Done INFO 09:21:53,476 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeInsertStatistics' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd.hist.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/isd.stats.dat' INFO 09:21:53,477 QGraph - Writing incremental jobs reports... INFO 09:21:53,487 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120044-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/2017120044-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:21:53,487 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-34.out INFO 09:22:32,293 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120057-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/2017120057-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:22:32,293 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-35.out INFO 09:23:12,806 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120074-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/2017120074-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:23:12,811 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-36.out INFO 09:23:49,350 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120079-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/2017120079-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:23:49,350 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-37.out INFO 09:24:28,901 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120090-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/2017120090-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:24:28,905 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-38.out INFO 09:25:07,192 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK2CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CK2CK4-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:25:07,192 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-39.out INFO 09:25:45,804 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK3-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CK3-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:25:45,804 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-40.out INFO 09:26:21,804 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CK4-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:26:21,804 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-41.out INFO 09:27:01,513 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK5-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CK5-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:27:01,517 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-42.out INFO 09:27:39,947 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120087-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120087-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:27:39,951 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-43.out INFO 09:28:15,909 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120089-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120089-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:28:15,910 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-44.out INFO 09:28:53,550 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120092-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120092-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:28:53,550 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-45.out INFO 09:29:29,402 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120093-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120093-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:29:29,402 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-46.out INFO 09:30:05,139 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120098-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120098-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:30:05,140 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-47.out INFO 09:30:43,426 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120106-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120106-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:30:43,427 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-48.out INFO 09:31:22,561 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120108-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120108-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:31:22,561 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-49.out INFO 09:32:02,075 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120111-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120111-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:32:02,075 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-50.out INFO 09:32:40,959 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120114-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120114-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:32:40,959 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-51.out INFO 09:33:19,466 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120115-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120115-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:33:19,466 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-52.out INFO 09:33:57,054 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120120-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120120-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:33:57,054 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-53.out INFO 09:34:35,451 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120121-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120121-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:34:35,451 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-54.out INFO 09:35:11,256 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120122-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120122-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:35:11,256 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-55.out INFO 09:35:51,031 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120123-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120123-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:35:51,031 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-56.out INFO 09:36:28,611 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120132-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120132-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 09:36:28,611 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-57.out INFO 09:37:08,046 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120044-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120044-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:37:08,046 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-59.out INFO 09:37:17,697 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120057-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120057-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:37:17,697 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-60.out INFO 09:37:28,391 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120074-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120074-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:37:28,392 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-61.out INFO 09:37:38,461 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120079-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120079-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:37:38,462 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-62.out INFO 09:37:48,615 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120090-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120090-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:37:48,615 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-63.out INFO 09:37:57,942 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK2CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK2CK4-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:37:57,942 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-64.out INFO 09:38:07,735 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK3-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK3-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:38:07,735 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-65.out INFO 09:38:17,397 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK4-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:38:17,397 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-66.out INFO 09:38:27,478 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK5-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK5-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:38:27,478 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-67.out INFO 09:38:38,458 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120087-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120087-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:38:38,458 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-68.out INFO 09:38:47,597 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120089-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120089-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:38:47,597 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-69.out INFO 09:38:56,487 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120092-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120092-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:38:56,488 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-70.out INFO 09:39:06,053 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120093-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120093-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:39:06,053 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-71.out INFO 09:39:15,376 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120098-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120098-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:39:15,376 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-72.out INFO 09:39:25,182 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120106-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120106-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:39:25,182 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-73.out INFO 09:39:35,420 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120108-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120108-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:39:35,420 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-74.out INFO 09:39:45,292 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120111-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120111-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:39:45,292 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-75.out INFO 09:39:55,138 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120114-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120114-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:39:55,138 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-76.out INFO 09:40:04,812 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120115-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120115-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:40:04,818 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-77.out INFO 09:40:14,183 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120120-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120120-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:40:14,183 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-78.out INFO 09:40:24,088 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120121-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120121-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:40:24,089 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-79.out INFO 09:40:34,581 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120122-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120122-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:40:34,581 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-80.out INFO 09:40:43,685 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120123-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120123-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:40:43,685 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-81.out INFO 09:40:53,511 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120132-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120132-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 09:40:53,511 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-82.out INFO 09:41:03,484 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120044-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120044-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:41:03,484 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-84.out INFO 09:42:04,871 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120057-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120057-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:42:04,875 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-85.out INFO 09:43:02,090 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120074-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120074-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:43:02,090 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-86.out INFO 09:43:58,697 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120079-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120079-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:43:58,697 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-87.out INFO 09:44:56,595 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120090-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120090-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:44:56,595 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-88.out INFO 09:45:51,128 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK2CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK2CK4-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:45:51,128 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-89.out INFO 09:46:49,059 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK3-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK3-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:46:49,059 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-90.out INFO 09:47:46,866 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK4-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:47:46,866 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-91.out INFO 09:48:49,244 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK5-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK5-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:48:49,244 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-92.out INFO 09:49:54,113 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120087-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120087-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:49:54,113 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-93.out INFO 09:50:53,583 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120089-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120089-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:50:53,583 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-94.out INFO 09:51:51,530 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120092-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120092-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:51:51,530 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-95.out INFO 09:52:49,168 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120093-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120093-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:52:49,168 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-96.out INFO 09:53:43,789 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120098-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120098-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:53:43,789 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-97.out INFO 09:54:41,212 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120106-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120106-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:54:41,213 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-98.out INFO 09:55:38,917 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120108-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120108-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:55:38,917 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-99.out INFO 09:56:39,929 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120111-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120111-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:56:39,929 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-100.out INFO 09:57:36,440 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120114-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120114-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:57:36,440 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-101.out INFO 09:58:30,823 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120115-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120115-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:58:30,823 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-102.out INFO 09:59:24,873 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120120-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120120-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 09:59:24,874 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-103.out INFO 10:00:23,215 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120121-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120121-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:00:23,215 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-104.out INFO 10:01:24,450 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120122-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120122-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:01:24,450 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-105.out INFO 10:02:19,262 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120123-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120123-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:02:19,262 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-106.out INFO 10:03:17,759 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120132-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120132-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:03:17,768 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-107.out INFO 10:04:20,285 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120044-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120044-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:04:20,285 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-109.out INFO 10:06:04,741 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120057-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120057-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:06:04,741 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-111.out INFO 10:07:54,221 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120074-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120074-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:07:54,221 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-113.out INFO 10:09:43,029 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120079-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120079-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:09:43,029 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-115.out INFO 10:11:32,001 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120090-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120090-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:11:32,001 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-117.out INFO 10:13:18,705 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK2CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK2CK4-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:13:18,705 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-119.out INFO 10:15:02,861 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK3-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK3-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:15:02,861 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-121.out INFO 10:16:45,613 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK4-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:16:45,613 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-123.out INFO 10:18:31,134 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK5-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK5-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:18:31,140 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-125.out INFO 10:20:16,838 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120087-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120087-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:20:16,838 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-127.out INFO 10:22:00,568 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120089-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120089-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:22:00,568 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-129.out INFO 10:23:43,968 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120092-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120092-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:23:43,968 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-131.out INFO 10:25:28,206 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120093-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120093-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:25:28,207 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-133.out INFO 10:27:14,881 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120098-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120098-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:27:14,881 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-135.out INFO 10:28:59,641 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120106-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120106-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:28:59,646 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-137.out INFO 10:30:45,150 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120108-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120108-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:30:45,150 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-139.out INFO 10:32:29,865 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120111-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120111-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:32:29,865 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-141.out INFO 10:34:21,495 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120114-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120114-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:34:21,495 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-143.out INFO 10:36:07,311 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120115-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120115-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:36:07,311 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-145.out INFO 10:37:50,945 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120120-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120120-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:37:50,945 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-147.out INFO 10:39:34,264 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120121-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120121-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:39:34,264 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-149.out INFO 10:41:19,699 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120122-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120122-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:41:19,699 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-151.out INFO 10:43:03,688 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120123-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120123-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:43:03,688 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-153.out INFO 10:44:47,865 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120132-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120132-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:44:47,865 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-155.out INFO 10:46:32,944 QGraph - 804 Pend, 96 Run, 1 Fail, 32 Done INFO 10:46:32,958 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120115-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120115-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,958 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK2CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CK2CK4-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,958 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK3-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK3-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,958 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120092-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120092-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,959 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120098-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120098-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,959 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120090-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120090-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,959 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120057-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120057-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,960 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120111-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120111-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,960 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK4-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,960 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120044-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120044-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,961 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120087-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120087-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,961 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120089-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120089-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,961 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120123-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120123-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,961 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120115-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120115-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,962 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120123-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120123-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,962 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120132-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120132-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,962 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120093-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120093-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,962 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120057-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/2017120057-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,963 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120132-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120132-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,963 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK3-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CK3-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,963 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK4-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,963 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120114-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120114-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,964 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK5-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK5-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,964 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120074-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/2017120074-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,964 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120093-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120093-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,964 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120098-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120098-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,965 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120120-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120120-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,965 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120079-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120079-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,966 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120089-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120089-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,966 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120057-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120057-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,966 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120087-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120087-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,966 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK5-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK5-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,967 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120106-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120106-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,967 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120044-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120044-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,967 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120108-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120108-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,967 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120122-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120122-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,968 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120090-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120090-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,968 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120132-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120132-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,968 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120098-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120098-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,968 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120121-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120121-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,969 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120120-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120120-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,969 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120123-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120123-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,969 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120111-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120111-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,969 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK3-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK3-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,970 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120074-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120074-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,970 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120087-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120087-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,970 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120108-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120108-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,970 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120106-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120106-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,971 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120079-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/2017120079-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,971 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120090-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120090-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,971 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120120-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120120-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,971 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120108-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120108-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,972 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120120-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120120-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,972 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120121-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120121-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,972 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120114-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120114-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,972 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK5-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CK5-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,972 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120087-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120087-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,973 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120093-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120093-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,973 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120122-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120122-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,973 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120044-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120044-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,973 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120121-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120121-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,974 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120079-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120079-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,974 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120106-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120106-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,975 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK2CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK2CK4-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,975 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120093-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120093-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,975 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120089-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120089-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,975 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK2CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK2CK4-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,976 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120115-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120115-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,976 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120132-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120132-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,976 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120111-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120111-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,977 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120090-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/2017120090-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,977 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120106-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120106-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,977 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120122-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120122-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,977 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK5-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK5-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,978 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK2CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK2CK4-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,978 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120079-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120079-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,978 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120089-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120089-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,978 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120115-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120115-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,979 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120108-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120108-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,979 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120074-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120074-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,979 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120057-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120057-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,980 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK4-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,980 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120122-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120122-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,980 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120111-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120111-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,980 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120114-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120114-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,981 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK3-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK3-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,981 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120092-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120092-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,981 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120092-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120092-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,981 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120123-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120123-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,982 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120092-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120092-IEMS.dedupped.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-referenceProfile' 'IEMS/metadata/gcprofile/reference.gcprof.zip' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-copyNumberMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.gcmask.fasta' '-insertSizeRadius' '10.0' INFO 10:46:32,982 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CK4-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CK4-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,982 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120074-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120074-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' INFO 10:46:32,982 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120098-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120098-IEMS.dedupped.spans.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-maxInsertSizeStandardDeviations' '3' ERROR 10:46:32,983 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120044-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/2017120044-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' ERROR 10:46:32,983 FunctionEdge - Contents of /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-34.out: INFO 09:21:57,414 HelpFormatter - ----------------------------------------------------------------------------------------- INFO 09:21:57,416 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7.GS-r1748-0-g74bfe0b, Compiled 2017/10/06 08:08:49 INFO 09:21:57,416 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute INFO 09:21:57,416 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk INFO 09:21:57,417 HelpFormatter - [Thu Feb 01 09:21:57 CST 2018] Executing on Linux 2.6.32-696.6.3.el6.x86_64 amd64 INFO 09:21:57,417 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_141-b15 INFO 09:21:57,420 HelpFormatter - Program Args: -T ComputeReadDepthCoverageWalker -R /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta -O /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/2017120044-IEMS.dedupped.depth.txt -disableGATKTraversal true -md IEMS/metadata -ploidyMapFile /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt -configFile conf/genstrip_parameters.txt -genomeMaskFile /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta -readDepthMaskFile /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed -minMapQ 10 -insertSizeRadius 10.0 INFO 09:21:57,422 HelpFormatter - Executing as wsh@localhost on Linux 2.6.32-696.6.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_141-b15. INFO 09:21:57,422 HelpFormatter - Date/Time: 2018/02/01 09:21:57 INFO 09:21:57,422 HelpFormatter - ----------------------------------------------------------------------------------------- INFO 09:21:57,422 HelpFormatter - ----------------------------------------------------------------------------------------- INFO 09:21:57,427 01-Feb-2018 GenomeAnalysisEngine - Strictness is SILENT INFO 09:21:57,534 01-Feb-2018 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 09:21:57,600 01-Feb-2018 GenomeAnalysisEngine - Preparing for traversal INFO 09:21:57,613 01-Feb-2018 GenomeAnalysisEngine - Done preparing for traversal INFO 09:21:57,613 01-Feb-2018 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 09:21:57,613 01-Feb-2018 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 09:21:57,613 01-Feb-2018 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime INFO 09:21:57,617 01-Feb-2018 MetaData - Opening metadata ... INFO 09:21:57,617 01-Feb-2018 MetaData - Adding metadata location IEMS/metadata ... INFO 09:21:57,619 01-Feb-2018 MetaData - Opened metadata. INFO 09:21:57,638 01-Feb-2018 MetaData - Loading insert size histograms ... INFO 09:21:57,686 01-Feb-2018 ComputeReadDepthCoverageWalker - Using genome mask /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta INFO 09:22:27,616 01-Feb-2018 ProgressMeter - Starting 0.0 30.0 s 49.6 w 100.0% 30.0 s 0.0 s INFO 09:22:32,275 01-Feb-2018 ProgressMeter - done 0.0 34.0 s 57.3 w 100.0% 34.0 s 0.0 s INFO 09:22:32,275 01-Feb-2018 ProgressMeter - Total runtime 34.66 secs, 0.58 min, 0.01 hours ------------------------------------------------------------------------------------------ Done. There were no warn messages. ------------------------------------------------------------------------------------------ INFO 10:46:32,983 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120121-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120121-IEMS.dedupped.rc.bin' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-configFile' 'conf/genstrip_parameters.txt' '-insertSizeRadius' '10.0' INFO 10:46:32,984 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/CX2017120114-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/CX2017120114-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 10:46:32,984 QGraph - Writing incremental jobs reports... INFO 10:46:32,994 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadSpanCoverage' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120044-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120057-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120074-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120079-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120090-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK2CK4-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK3-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK4-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK5-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120087-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120089-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120092-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120093-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120098-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120106-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120108-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120111-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120114-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120115-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120120-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120121-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120122-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120123-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120132-IEMS.dedupped.spans.txt' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans.dat' INFO 10:46:32,994 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-83.out INFO 10:46:36,748 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeGCProfiles' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120044-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120057-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120074-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120079-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120090-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK2CK4-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK3-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK4-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK5-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120087-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120089-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120092-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120093-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120098-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120106-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120108-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120111-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120114-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120115-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120120-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120121-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120122-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120123-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120132-IEMS.dedupped.bam.gcprof.zip' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofiles.zip' INFO 10:46:36,748 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-108.out INFO 10:46:40,648 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120044-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120044-IEMS.dedupped.rc.bin.idx' INFO 10:46:40,648 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-110.out INFO 10:47:55,468 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120057-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120057-IEMS.dedupped.rc.bin.idx' INFO 10:47:55,468 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-112.out INFO 10:49:10,509 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120074-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120074-IEMS.dedupped.rc.bin.idx' INFO 10:49:10,509 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-114.out INFO 10:50:29,109 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120079-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120079-IEMS.dedupped.rc.bin.idx' INFO 10:50:29,109 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-116.out INFO 10:51:47,318 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120090-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120090-IEMS.dedupped.rc.bin.idx' INFO 10:51:47,318 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-118.out INFO 10:53:02,792 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK2CK4-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK2CK4-IEMS.dedupped.rc.bin.idx' INFO 10:53:02,792 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-120.out INFO 10:54:14,730 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK3-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK3-IEMS.dedupped.rc.bin.idx' INFO 10:54:14,730 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-122.out INFO 10:55:25,996 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK4-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK4-IEMS.dedupped.rc.bin.idx' INFO 10:55:26,001 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-124.out INFO 10:56:37,296 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK5-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK5-IEMS.dedupped.rc.bin.idx' INFO 10:56:37,296 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-126.out INFO 10:57:48,170 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120087-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120087-IEMS.dedupped.rc.bin.idx' INFO 10:57:48,170 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-128.out INFO 10:59:01,143 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120089-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120089-IEMS.dedupped.rc.bin.idx' INFO 10:59:01,143 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-130.out INFO 11:00:13,440 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120092-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120092-IEMS.dedupped.rc.bin.idx' INFO 11:00:13,441 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-132.out INFO 11:01:25,117 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120093-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120093-IEMS.dedupped.rc.bin.idx' INFO 11:01:25,117 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-134.out INFO 11:02:38,191 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120098-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120098-IEMS.dedupped.rc.bin.idx' INFO 11:02:38,191 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-136.out INFO 11:03:49,273 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120106-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120106-IEMS.dedupped.rc.bin.idx' INFO 11:03:49,273 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-138.out INFO 11:05:00,879 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120108-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120108-IEMS.dedupped.rc.bin.idx' INFO 11:05:00,879 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-140.out INFO 11:06:13,091 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120111-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120111-IEMS.dedupped.rc.bin.idx' INFO 11:06:13,091 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-142.out INFO 11:07:24,201 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120114-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120114-IEMS.dedupped.rc.bin.idx' INFO 11:07:24,202 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-144.out INFO 11:08:35,719 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120115-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120115-IEMS.dedupped.rc.bin.idx' INFO 11:08:35,719 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-146.out INFO 11:09:47,659 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120120-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120120-IEMS.dedupped.rc.bin.idx' INFO 11:09:47,659 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-148.out INFO 11:10:59,498 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120121-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120121-IEMS.dedupped.rc.bin.idx' INFO 11:10:59,504 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-150.out INFO 11:12:16,625 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120122-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120122-IEMS.dedupped.rc.bin.idx' INFO 11:12:16,625 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-152.out INFO 11:13:27,842 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120123-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120123-IEMS.dedupped.rc.bin.idx' INFO 11:13:27,842 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-154.out INFO 11:14:39,312 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120132-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120132-IEMS.dedupped.rc.bin.idx' INFO 11:14:39,312 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-156.out INFO 11:15:50,497 QGraph - 778 Pend, 26 Run, 2 Fail, 127 Done INFO 11:15:50,498 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120121-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120121-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,498 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120114-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120114-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,498 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120090-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120090-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,499 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadSpanCoverage' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120044-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120057-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120074-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120079-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/2017120090-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK2CK4-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK3-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK4-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CK5-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120087-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120089-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120092-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120093-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120098-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120106-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120108-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120111-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120114-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120115-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120120-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120121-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120122-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120123-IEMS.dedupped.spans.txt' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans/CX2017120132-IEMS.dedupped.spans.txt' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/spans.dat' INFO 11:15:50,499 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120074-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120074-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,499 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120115-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120115-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,499 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK5-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK5-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,500 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK2CK4-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK2CK4-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,500 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120106-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120106-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,500 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120093-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120093-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,500 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120122-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120122-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,501 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120092-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120092-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,501 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK3-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK3-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,501 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120108-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120108-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,502 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120123-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120123-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,502 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120044-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120044-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,502 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120098-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120098-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,502 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120057-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120057-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,503 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120087-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120087-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,503 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120079-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120079-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,503 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120120-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120120-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,503 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120132-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120132-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,503 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK4-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK4-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,504 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120089-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120089-IEMS.dedupped.rc.bin.idx' ERROR 11:15:50,504 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeGCProfiles' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120044-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120057-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120074-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120079-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120090-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK2CK4-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK3-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK4-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK5-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120087-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120089-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120092-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120093-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120098-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120106-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120108-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120111-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120114-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120115-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120120-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120121-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120122-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120123-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120132-IEMS.dedupped.bam.gcprof.zip' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofiles.zip' ERROR 11:15:50,504 FunctionEdge - Contents of /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-108.out: INFO 10:46:40,468 HelpFormatter - -------------------------------------------------------- INFO 10:46:40,469 HelpFormatter - Program Name: org.broadinstitute.sv.apps.MergeGCProfiles INFO 10:46:40,473 HelpFormatter - Program Args: -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120044-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120057-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120074-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120079-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120090-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK2CK4-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK3-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK4-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK5-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120087-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120089-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120092-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120093-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120098-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120106-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120108-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120111-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120114-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120115-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120120-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120121-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120122-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120123-IEMS.dedupped.bam.gcprof.zip -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120132-IEMS.dedupped.bam.gcprof.zip -O /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofiles.zip INFO 10:46:40,474 HelpFormatter - Executing as wsh@localhost on Linux 2.6.32-696.6.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_141-b15. INFO 10:46:40,475 HelpFormatter - Date/Time: 2018/02/01 10:46:40 INFO 10:46:40,475 HelpFormatter - -------------------------------------------------------- INFO 10:46:40,475 HelpFormatter - -------------------------------------------------------- INFO 10:46:40,616 CommandLineProgram - Program completed. ------------------------------------------------------------------------------------------ Done. There were no warn messages. ------------------------------------------------------------------------------------------ INFO 11:15:50,505 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120111-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120111-IEMS.dedupped.rc.bin.idx' INFO 11:15:50,505 QGraph - Writing incremental jobs reports... INFO 11:15:50,515 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.queue.WriteFileList' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120044-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120057-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120074-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120079-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120090-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK2CK4-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK3-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK4-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK5-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120087-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120089-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120092-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120093-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120098-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120106-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120108-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120111-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120114-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120115-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120120-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120121-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120122-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120123-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120132-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' INFO 11:15:50,515 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-157.out INFO 11:15:54,192 QGraph - 777 Pend, 1 Run, 3 Fail, 152 Done INFO 11:16:20,515 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.queue.WriteFileList' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120044-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120057-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120074-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120079-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/2017120090-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK2CK4-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK3-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK4-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CK5-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120087-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120089-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120092-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120093-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120098-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120106-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120108-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120111-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120114-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120115-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120120-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120121-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120122-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120123-IEMS.dedupped.rc.bin' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache/CX2017120132-IEMS.dedupped.rc.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' INFO 11:16:20,515 QGraph - Writing incremental jobs reports... INFO 11:16:20,528 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0001.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:1-10000000 INFO 11:16:20,528 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-158.out INFO 11:16:35,515 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0002.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:10000001-20000000 INFO 11:16:35,515 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-160.out INFO 11:16:49,482 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0003.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:20000001-30000000 INFO 11:16:49,482 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-162.out INFO 11:17:04,857 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0004.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:30000001-40000000 INFO 11:17:04,858 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-164.out INFO 11:17:18,402 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0005.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:40000001-50000000 INFO 11:17:18,402 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-166.out INFO 11:17:33,842 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0006.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:50000001-60000000 INFO 11:17:33,843 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-168.out INFO 11:17:48,211 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0007.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:60000001-70000000 INFO 11:17:48,211 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-170.out INFO 11:18:02,293 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0008.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:70000001-80000000 INFO 11:18:02,293 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-172.out INFO 11:18:16,040 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0009.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:80000001-90000000 INFO 11:18:16,040 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-174.out INFO 11:18:30,606 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0010.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:90000001-100000000 INFO 11:18:30,606 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-176.out INFO 11:18:44,985 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0011.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:100000001-110000000 INFO 11:18:44,985 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-178.out INFO 11:19:00,020 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0012.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:110000001-120000000 INFO 11:19:00,020 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-180.out INFO 11:19:14,572 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0013.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:120000001-130000000 INFO 11:19:14,572 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-182.out INFO 11:19:29,047 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0014.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:130000001-140000000 INFO 11:19:29,047 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-184.out INFO 11:19:43,159 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0015.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:140000001-150000000 INFO 11:19:43,159 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-186.out INFO 11:19:57,654 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0016.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:150000001-160000000 INFO 11:19:57,655 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-188.out INFO 11:20:13,039 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0017.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:160000001-170000000 INFO 11:20:13,039 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-190.out INFO 11:20:27,122 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0018.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:170000001-180000000 INFO 11:20:27,123 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-192.out INFO 11:20:40,436 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0019.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:180000001-190000000 INFO 11:20:40,436 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-194.out INFO 11:20:54,822 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0020.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:190000001-200000000 INFO 11:20:54,822 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-196.out INFO 11:21:08,909 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0021.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:200000001-210000000 INFO 11:21:08,909 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-198.out INFO 11:21:22,461 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0022.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:210000001-220000000 INFO 11:21:22,461 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-200.out INFO 11:21:36,915 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0023.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:220000001-230000000 INFO 11:21:36,915 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-202.out INFO 11:21:52,231 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0024.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:230000001-240000000 INFO 11:21:52,231 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-204.out INFO 11:22:07,054 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0025.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:240000001-249250621 -L 2:1-10000000 INFO 11:22:07,055 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-206.out INFO 11:22:31,509 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0026.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:10000001-20000000 INFO 11:22:31,510 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-208.out INFO 11:22:46,581 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0027.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:20000001-30000000 INFO 11:22:46,581 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-210.out INFO 11:23:01,252 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0028.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:30000001-40000000 INFO 11:23:01,252 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-212.out INFO 11:23:15,746 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0029.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:40000001-50000000 INFO 11:23:15,746 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-214.out INFO 11:23:30,039 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0030.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:50000001-60000000 INFO 11:23:30,039 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-216.out INFO 11:23:44,512 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0031.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:60000001-70000000 INFO 11:23:44,512 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-218.out INFO 11:23:57,967 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0032.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:70000001-80000000 INFO 11:23:57,967 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-220.out INFO 11:24:11,480 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0033.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:80000001-90000000 INFO 11:24:11,480 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-222.out INFO 11:24:25,856 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0034.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:90000001-100000000 INFO 11:24:25,856 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-224.out INFO 11:24:40,459 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0035.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:100000001-110000000 INFO 11:24:40,460 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-226.out INFO 11:24:54,505 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0036.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:110000001-120000000 INFO 11:24:54,505 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-228.out INFO 11:25:08,166 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0037.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:120000001-130000000 INFO 11:25:08,166 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-230.out INFO 11:25:22,507 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0038.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:130000001-140000000 INFO 11:25:22,507 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-232.out INFO 11:25:36,525 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0039.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:140000001-150000000 INFO 11:25:36,525 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-234.out INFO 11:25:50,160 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0040.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:150000001-160000000 INFO 11:25:50,160 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-236.out INFO 11:26:04,724 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0041.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:160000001-170000000 INFO 11:26:04,724 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-238.out INFO 11:26:18,918 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0042.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:170000001-180000000 INFO 11:26:18,918 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-240.out INFO 11:26:33,321 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0043.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:180000001-190000000 INFO 11:26:33,321 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-242.out INFO 11:26:46,997 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0044.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:190000001-200000000 INFO 11:26:46,997 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-244.out INFO 11:27:01,101 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0045.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:200000001-210000000 INFO 11:27:01,102 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-246.out INFO 11:27:15,575 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0046.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:210000001-220000000 INFO 11:27:15,575 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-248.out INFO 11:27:33,774 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0047.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:220000001-230000000 INFO 11:27:33,774 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-250.out INFO 11:27:48,023 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0048.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:230000001-240000000 INFO 11:27:48,024 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-252.out INFO 11:28:03,002 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0049.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:240000001-243199373 -L 3:1-10000000 INFO 11:28:03,002 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-254.out INFO 11:28:20,147 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0050.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:10000001-20000000 INFO 11:28:20,148 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-256.out INFO 11:28:33,762 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0051.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:20000001-30000000 INFO 11:28:33,762 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-258.out INFO 11:28:48,494 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0052.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:30000001-40000000 INFO 11:28:48,494 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-260.out INFO 11:29:02,755 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0053.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:40000001-50000000 INFO 11:29:02,755 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-262.out INFO 11:29:16,636 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0054.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:50000001-60000000 INFO 11:29:16,636 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-264.out INFO 11:29:30,051 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0055.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:60000001-70000000 INFO 11:29:30,051 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-266.out INFO 11:29:44,670 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0056.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:70000001-80000000 INFO 11:29:44,671 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-268.out INFO 11:29:58,327 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0057.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:80000001-90000000 INFO 11:29:58,327 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-270.out INFO 11:30:12,143 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0058.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:90000001-100000000 INFO 11:30:12,143 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-272.out INFO 11:30:26,864 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0059.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:100000001-110000000 INFO 11:30:26,864 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-274.out INFO 11:30:40,798 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0060.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:110000001-120000000 INFO 11:30:40,798 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-276.out INFO 11:30:54,597 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0061.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:120000001-130000000 INFO 11:30:54,597 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-278.out INFO 11:31:08,909 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0062.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:130000001-140000000 INFO 11:31:08,909 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-280.out INFO 11:31:23,149 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0063.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:140000001-150000000 INFO 11:31:23,149 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-282.out INFO 11:31:36,937 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0064.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:150000001-160000000 INFO 11:31:36,937 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-284.out INFO 11:31:51,106 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0065.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:160000001-170000000 INFO 11:31:51,106 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-286.out INFO 11:32:05,364 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0066.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:170000001-180000000 INFO 11:32:05,364 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-288.out INFO 11:32:19,175 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0067.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:180000001-190000000 INFO 11:32:19,175 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-290.out INFO 11:32:33,620 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0068.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:190000001-198022430 -L 4:1-10000000 INFO 11:32:33,620 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-292.out INFO 11:32:55,624 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0069.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:10000001-20000000 INFO 11:32:55,629 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-294.out INFO 11:33:10,169 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0070.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:20000001-30000000 INFO 11:33:10,169 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-296.out INFO 11:33:24,483 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0071.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:30000001-40000000 INFO 11:33:24,483 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-298.out INFO 11:33:38,665 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0072.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:40000001-50000000 INFO 11:33:38,665 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-300.out INFO 11:33:52,089 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0073.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:50000001-60000000 INFO 11:33:52,089 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-302.out INFO 11:34:09,322 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0074.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:60000001-70000000 INFO 11:34:09,322 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-304.out INFO 11:34:23,151 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0075.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:70000001-80000000 INFO 11:34:23,151 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-306.out INFO 11:34:36,870 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0076.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:80000001-90000000 INFO 11:34:36,870 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-308.out INFO 11:34:50,459 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0077.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:90000001-100000000 INFO 11:34:50,459 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-310.out INFO 11:35:03,975 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0078.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:100000001-110000000 INFO 11:35:03,975 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-312.out INFO 11:35:18,724 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0079.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:110000001-120000000 INFO 11:35:18,724 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-314.out INFO 11:35:32,679 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0080.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:120000001-130000000 INFO 11:35:32,679 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-316.out INFO 11:35:46,948 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0081.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:130000001-140000000 INFO 11:35:46,948 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-318.out INFO 11:36:01,045 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0082.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:140000001-150000000 INFO 11:36:01,046 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-320.out INFO 11:36:14,833 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0083.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:150000001-160000000 INFO 11:36:14,833 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-322.out INFO 11:36:28,866 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0084.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:160000001-170000000 INFO 11:36:28,866 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-324.out INFO 11:36:42,777 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0085.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:170000001-180000000 INFO 11:36:42,777 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-326.out INFO 11:36:57,005 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0086.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:180000001-190000000 INFO 11:36:57,005 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-328.out INFO 11:37:11,060 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0087.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:190000001-191154276 -L 5:1-10000000 INFO 11:37:11,060 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-330.out INFO 11:37:26,337 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0088.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:10000001-20000000 INFO 11:37:26,337 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-332.out INFO 11:37:40,994 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0089.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:20000001-30000000 INFO 11:37:40,994 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-334.out INFO 11:37:55,726 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0090.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:30000001-40000000 INFO 11:37:55,726 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-336.out INFO 11:38:10,409 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0091.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:40000001-50000000 INFO 11:38:10,409 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-338.out INFO 11:38:23,882 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0092.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:50000001-60000000 INFO 11:38:23,882 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-340.out INFO 11:38:38,323 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0093.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:60000001-70000000 INFO 11:38:38,323 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-342.out INFO 11:38:53,179 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0094.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:70000001-80000000 INFO 11:38:53,179 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-344.out INFO 11:39:07,634 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0095.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:80000001-90000000 INFO 11:39:07,634 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-346.out INFO 11:39:22,489 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0096.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:90000001-100000000 INFO 11:39:22,489 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-348.out INFO 11:39:36,488 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0097.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:100000001-110000000 INFO 11:39:36,489 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-350.out INFO 11:39:50,460 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0098.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:110000001-120000000 INFO 11:39:50,460 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-352.out INFO 11:40:05,401 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0099.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:120000001-130000000 INFO 11:40:05,406 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-354.out INFO 11:40:19,457 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0100.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:130000001-140000000 INFO 11:40:19,457 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-356.out INFO 11:40:33,409 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0101.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:140000001-150000000 INFO 11:40:33,409 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-358.out INFO 11:40:46,905 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0102.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:150000001-160000000 INFO 11:40:46,905 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-360.out INFO 11:41:01,471 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0103.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:160000001-170000000 INFO 11:41:01,471 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-362.out INFO 11:41:15,140 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0104.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:170000001-180000000 INFO 11:41:15,140 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-364.out INFO 11:41:28,783 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0105.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:180000001-180915260 -L 6:1-10000000 INFO 11:41:28,783 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-366.out INFO 11:41:43,498 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0106.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:10000001-20000000 INFO 11:41:43,499 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-368.out INFO 11:41:58,165 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0107.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:20000001-30000000 INFO 11:41:58,165 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-370.out INFO 11:42:12,994 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0108.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:30000001-40000000 INFO 11:42:12,994 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-372.out INFO 11:42:26,922 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0109.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:40000001-50000000 INFO 11:42:26,922 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-374.out INFO 11:42:43,867 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0110.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:50000001-60000000 INFO 11:42:43,867 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-376.out INFO 11:42:57,860 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0111.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:60000001-70000000 INFO 11:42:57,860 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-378.out INFO 11:43:12,636 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0112.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:70000001-80000000 INFO 11:43:12,636 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-380.out INFO 11:43:26,944 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0113.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:80000001-90000000 INFO 11:43:26,944 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-382.out INFO 11:43:41,998 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0114.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:90000001-100000000 INFO 11:43:41,998 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-384.out INFO 11:43:56,286 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0115.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:100000001-110000000 INFO 11:43:56,287 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-386.out INFO 11:44:10,381 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0116.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:110000001-120000000 INFO 11:44:10,381 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-388.out INFO 11:44:24,652 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0117.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:120000001-130000000 INFO 11:44:24,652 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-390.out INFO 11:44:37,905 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0118.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:130000001-140000000 INFO 11:44:37,905 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-392.out INFO 11:44:52,046 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0119.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:140000001-150000000 INFO 11:44:52,046 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-394.out INFO 11:45:07,283 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0120.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:150000001-160000000 INFO 11:45:07,283 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-396.out INFO 11:45:21,357 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0121.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:160000001-170000000 INFO 11:45:21,357 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-398.out INFO 11:45:35,320 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0122.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:170000001-171115067 -L 7:1-10000000 INFO 11:45:35,320 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-400.out INFO 11:45:50,793 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0123.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:10000001-20000000 INFO 11:45:50,793 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-402.out INFO 11:46:04,923 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0124.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:20000001-30000000 INFO 11:46:04,923 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-404.out INFO 11:46:19,142 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0125.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:30000001-40000000 INFO 11:46:19,142 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-406.out INFO 11:46:33,356 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0126.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:40000001-50000000 INFO 11:46:33,356 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-408.out INFO 11:46:47,950 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0127.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:50000001-60000000 INFO 11:46:47,950 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-410.out INFO 11:47:02,332 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0128.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:60000001-70000000 INFO 11:47:02,332 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-412.out INFO 11:47:16,793 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0129.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:70000001-80000000 INFO 11:47:16,793 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-414.out INFO 11:47:31,181 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0130.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:80000001-90000000 INFO 11:47:31,181 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-416.out INFO 11:47:48,070 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0131.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:90000001-100000000 INFO 11:47:48,070 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-418.out INFO 11:48:01,767 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0132.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:100000001-110000000 INFO 11:48:01,768 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-420.out INFO 11:48:16,079 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0133.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:110000001-120000000 INFO 11:48:16,079 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-422.out INFO 11:48:30,386 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0134.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:120000001-130000000 INFO 11:48:30,386 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-424.out INFO 11:48:45,345 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0135.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:130000001-140000000 INFO 11:48:45,345 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-426.out INFO 11:49:00,194 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0136.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:140000001-150000000 INFO 11:49:00,194 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-428.out INFO 11:49:14,188 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0137.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:150000001-159138663 -L X:1-10000000 INFO 11:49:14,188 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-430.out INFO 11:49:38,004 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0138.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:10000001-20000000 INFO 11:49:38,004 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-432.out INFO 11:49:51,562 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0139.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:20000001-30000000 INFO 11:49:51,562 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-434.out INFO 11:50:05,679 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0140.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:30000001-40000000 INFO 11:50:05,679 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-436.out INFO 11:50:19,774 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0141.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:40000001-50000000 INFO 11:50:19,774 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-438.out INFO 11:50:33,139 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0142.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:50000001-60000000 INFO 11:50:33,139 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-440.out INFO 11:50:47,210 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0143.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:60000001-70000000 INFO 11:50:47,210 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-442.out INFO 11:51:02,079 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0144.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:70000001-80000000 INFO 11:51:02,079 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-444.out INFO 11:51:15,681 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0145.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:80000001-90000000 INFO 11:51:15,681 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-446.out INFO 11:51:29,252 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0146.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:90000001-100000000 INFO 11:51:29,252 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-448.out INFO 11:51:42,262 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0147.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:100000001-110000000 INFO 11:51:42,262 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-450.out INFO 11:51:55,959 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0148.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:110000001-120000000 INFO 11:51:55,959 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-452.out INFO 11:52:09,475 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0149.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:120000001-130000000 INFO 11:52:09,475 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-454.out INFO 11:52:23,345 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0150.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:130000001-140000000 INFO 11:52:23,345 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-456.out INFO 11:52:37,397 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0151.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:140000001-150000000 INFO 11:52:37,397 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-458.out INFO 11:52:51,974 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0152.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:150000001-155270560 -L 8:1-10000000 INFO 11:52:51,974 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-460.out INFO 11:53:11,945 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0153.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:10000001-20000000 INFO 11:53:11,945 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-462.out INFO 11:53:26,163 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0154.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:20000001-30000000 INFO 11:53:26,163 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-464.out INFO 11:53:40,718 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0155.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:30000001-40000000 INFO 11:53:40,718 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-466.out INFO 11:53:55,072 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0156.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:40000001-50000000 INFO 11:53:55,072 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-468.out INFO 11:54:09,793 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0157.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:50000001-60000000 INFO 11:54:09,793 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-470.out INFO 11:54:24,296 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0158.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:60000001-70000000 INFO 11:54:24,296 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-472.out INFO 11:54:38,344 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0159.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:70000001-80000000 INFO 11:54:38,344 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-474.out INFO 11:54:53,870 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0160.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:80000001-90000000 INFO 11:54:53,870 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-476.out INFO 11:55:08,090 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0161.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:90000001-100000000 INFO 11:55:08,090 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-478.out INFO 11:55:22,172 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0162.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:100000001-110000000 INFO 11:55:22,172 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-480.out INFO 11:55:36,521 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0163.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:110000001-120000000 INFO 11:55:36,521 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-482.out INFO 11:55:50,988 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0164.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:120000001-130000000 INFO 11:55:50,988 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-484.out INFO 11:56:05,038 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0165.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:130000001-140000000 INFO 11:56:05,038 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-486.out INFO 11:56:19,544 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0166.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:140000001-146364022 -L 9:1-10000000 INFO 11:56:19,544 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-488.out INFO 11:56:40,090 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0167.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:10000001-20000000 INFO 11:56:40,091 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-490.out INFO 11:56:54,677 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0168.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:20000001-30000000 INFO 11:56:54,677 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-492.out INFO 11:57:09,482 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0169.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:30000001-40000000 INFO 11:57:09,482 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-494.out INFO 11:57:24,348 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0170.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:40000001-50000000 INFO 11:57:24,348 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-496.out INFO 11:57:38,455 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0171.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:50000001-60000000 INFO 11:57:38,455 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-498.out INFO 11:57:52,357 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0172.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:60000001-70000000 INFO 11:57:52,357 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-500.out INFO 11:58:08,148 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0173.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:70000001-80000000 INFO 11:58:08,148 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-502.out INFO 11:58:22,695 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0174.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:80000001-90000000 INFO 11:58:22,695 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-504.out INFO 11:58:36,520 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0175.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:90000001-100000000 INFO 11:58:36,520 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-506.out INFO 11:58:50,690 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0176.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:100000001-110000000 INFO 11:58:50,690 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-508.out INFO 11:59:05,714 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0177.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:110000001-120000000 INFO 11:59:05,714 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-510.out INFO 11:59:23,872 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0178.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:120000001-130000000 INFO 11:59:23,872 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-512.out INFO 11:59:38,001 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0179.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:130000001-140000000 INFO 11:59:38,001 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-514.out INFO 11:59:51,847 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0180.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:140000001-141213431 -L 10:1-10000000 INFO 11:59:51,847 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-516.out INFO 12:00:06,847 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0181.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:10000001-20000000 INFO 12:00:06,852 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-518.out INFO 12:00:20,977 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0182.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:20000001-30000000 INFO 12:00:20,977 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-520.out INFO 12:00:35,801 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0183.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:30000001-40000000 INFO 12:00:35,801 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-522.out INFO 12:00:49,215 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0184.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:40000001-50000000 INFO 12:00:49,215 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-524.out INFO 12:01:03,704 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0185.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:50000001-60000000 INFO 12:01:03,704 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-526.out INFO 12:01:17,789 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0186.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:60000001-70000000 INFO 12:01:17,789 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-528.out INFO 12:01:31,828 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0187.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:70000001-80000000 INFO 12:01:31,828 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-530.out INFO 12:01:45,381 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0188.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:80000001-90000000 INFO 12:01:45,381 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-532.out INFO 12:01:59,259 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0189.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:90000001-100000000 INFO 12:01:59,259 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-534.out INFO 12:02:13,042 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0190.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:100000001-110000000 INFO 12:02:13,042 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-536.out INFO 12:02:27,039 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0191.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:110000001-120000000 INFO 12:02:27,039 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-538.out INFO 12:02:41,395 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0192.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:120000001-130000000 INFO 12:02:41,395 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-540.out INFO 12:02:59,527 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0193.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:130000001-135534747 -L 11:1-10000000 INFO 12:02:59,528 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-542.out INFO 12:03:18,546 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0194.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:10000001-20000000 INFO 12:03:18,546 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-544.out INFO 12:03:32,553 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0195.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:20000001-30000000 INFO 12:03:32,553 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-546.out INFO 12:03:46,936 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0196.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:30000001-40000000 INFO 12:03:46,936 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-548.out INFO 12:04:00,246 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0197.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:40000001-50000000 INFO 12:04:00,246 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-550.out INFO 12:04:13,780 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0198.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:50000001-60000000 INFO 12:04:13,780 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-552.out INFO 12:04:27,946 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0199.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:60000001-70000000 INFO 12:04:27,946 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-554.out INFO 12:04:41,586 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0200.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:70000001-80000000 INFO 12:04:41,586 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-556.out INFO 12:04:55,241 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0201.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:80000001-90000000 INFO 12:04:55,241 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-558.out INFO 12:05:09,584 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0202.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:90000001-100000000 INFO 12:05:09,584 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-560.out INFO 12:05:24,327 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0203.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:100000001-110000000 INFO 12:05:24,327 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-562.out INFO 12:05:42,527 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0204.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:110000001-120000000 INFO 12:05:42,527 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-564.out INFO 12:05:55,848 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0205.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:120000001-130000000 INFO 12:05:55,849 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-566.out INFO 12:06:09,347 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0206.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:130000001-135006516 -L 12:1-10000000 INFO 12:06:09,347 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-568.out INFO 12:06:28,456 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0207.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:10000001-20000000 INFO 12:06:28,456 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-570.out INFO 12:06:42,833 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0208.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:20000001-30000000 INFO 12:06:42,834 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-572.out INFO 12:06:56,917 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0209.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:30000001-40000000 INFO 12:06:56,917 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-574.out INFO 12:07:11,126 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0210.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:40000001-50000000 INFO 12:07:11,126 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-576.out INFO 12:07:24,659 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0211.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:50000001-60000000 INFO 12:07:24,659 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-578.out INFO 12:07:38,600 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0212.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:60000001-70000000 INFO 12:07:38,600 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-580.out INFO 12:07:53,072 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0213.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:70000001-80000000 INFO 12:07:53,072 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-582.out INFO 12:08:06,992 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0214.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:80000001-90000000 INFO 12:08:06,992 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-584.out INFO 12:08:21,184 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0215.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:90000001-100000000 INFO 12:08:21,184 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-586.out INFO 12:08:35,699 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0216.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:100000001-110000000 INFO 12:08:35,699 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-588.out INFO 12:08:49,579 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0217.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:110000001-120000000 INFO 12:08:49,579 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-590.out INFO 12:09:03,267 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0218.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:120000001-130000000 INFO 12:09:03,268 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-592.out INFO 12:09:17,069 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0219.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:130000001-133851895 -L 13:1-10000000 INFO 12:09:17,069 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-594.out INFO 12:09:34,756 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0220.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:10000001-20000000 INFO 12:09:34,756 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-596.out INFO 12:09:51,477 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0221.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:20000001-30000000 INFO 12:09:51,477 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-598.out INFO 12:10:06,275 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0222.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:30000001-40000000 INFO 12:10:06,275 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-600.out INFO 12:10:20,607 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0223.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:40000001-50000000 INFO 12:10:20,607 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-602.out INFO 12:10:35,097 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0224.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:50000001-60000000 INFO 12:10:35,097 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-604.out INFO 12:10:49,142 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0225.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:60000001-70000000 INFO 12:10:49,142 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-606.out INFO 12:11:03,090 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0226.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:70000001-80000000 INFO 12:11:03,090 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-608.out INFO 12:11:17,619 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0227.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:80000001-90000000 INFO 12:11:17,619 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-610.out INFO 12:11:32,702 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0228.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:90000001-100000000 INFO 12:11:32,702 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-612.out INFO 12:11:47,285 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0229.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:100000001-110000000 INFO 12:11:47,286 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-614.out INFO 12:12:01,633 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0230.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:110000001-115169878 -L 14:1-10000000 INFO 12:12:01,633 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-616.out INFO 12:12:20,914 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0231.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:10000001-20000000 INFO 12:12:20,914 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-618.out INFO 12:12:35,601 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0232.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:20000001-30000000 INFO 12:12:35,601 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-620.out INFO 12:12:49,284 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0233.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:30000001-40000000 INFO 12:12:49,284 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-622.out INFO 12:13:03,825 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0234.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:40000001-50000000 INFO 12:13:03,825 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-624.out INFO 12:13:18,736 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0235.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:50000001-60000000 INFO 12:13:18,736 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-626.out INFO 12:13:33,576 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0236.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:60000001-70000000 INFO 12:13:33,576 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-628.out INFO 12:13:51,287 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0237.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:70000001-80000000 INFO 12:13:51,287 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-630.out INFO 12:14:04,978 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0238.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:80000001-90000000 INFO 12:14:04,978 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-632.out INFO 12:14:18,515 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0239.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:90000001-100000000 INFO 12:14:18,515 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-634.out INFO 12:14:32,607 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0240.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:100000001-107349540 -L 15:1-10000000 INFO 12:14:32,607 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-636.out INFO 12:14:53,520 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0241.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:10000001-20000000 INFO 12:14:53,520 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-638.out INFO 12:15:07,190 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0242.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:20000001-30000000 INFO 12:15:07,190 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-640.out INFO 12:15:23,017 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0243.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:30000001-40000000 INFO 12:15:23,017 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-642.out INFO 12:15:36,696 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0244.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:40000001-50000000 INFO 12:15:36,696 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-644.out INFO 12:15:50,458 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0245.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:50000001-60000000 INFO 12:15:50,459 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-646.out INFO 12:16:04,501 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0246.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:60000001-70000000 INFO 12:16:04,501 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-648.out INFO 12:16:18,794 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0247.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:70000001-80000000 INFO 12:16:18,794 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-650.out INFO 12:16:32,991 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0248.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:80000001-90000000 INFO 12:16:32,991 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-652.out INFO 12:16:47,104 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0249.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:90000001-100000000 INFO 12:16:47,104 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-654.out INFO 12:17:01,353 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0250.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:100000001-102531392 -L 16:1-10000000 INFO 12:17:01,353 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-656.out INFO 12:17:17,653 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0251.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:10000001-20000000 INFO 12:17:17,653 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-658.out INFO 12:17:32,591 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0252.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:20000001-30000000 INFO 12:17:32,592 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-660.out INFO 12:17:47,219 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0253.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:30000001-40000000 INFO 12:17:47,219 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-662.out INFO 12:18:01,526 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0254.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:40000001-50000000 INFO 12:18:01,526 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-664.out INFO 12:18:17,627 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0255.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:50000001-60000000 INFO 12:18:17,627 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-666.out INFO 12:18:32,239 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0256.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:60000001-70000000 INFO 12:18:32,239 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-668.out INFO 12:18:46,780 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0257.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:70000001-80000000 INFO 12:18:46,780 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-670.out INFO 12:19:01,055 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0258.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:80000001-90000000 INFO 12:19:01,055 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-672.out INFO 12:19:15,071 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0259.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:90000001-90354753 -L 17:1-10000000 INFO 12:19:15,071 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-674.out INFO 12:19:29,421 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0260.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:10000001-20000000 INFO 12:19:29,421 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-676.out INFO 12:19:48,570 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0261.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:20000001-30000000 INFO 12:19:48,570 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-678.out INFO 12:20:02,511 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0262.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:30000001-40000000 INFO 12:20:02,511 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-680.out INFO 12:20:16,122 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0263.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:40000001-50000000 INFO 12:20:16,122 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-682.out INFO 12:20:33,000 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0264.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:50000001-60000000 INFO 12:20:33,000 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-684.out INFO 12:20:47,370 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0265.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:60000001-70000000 INFO 12:20:47,371 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-686.out INFO 12:21:01,647 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0266.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:70000001-80000000 INFO 12:21:01,647 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-688.out INFO 12:21:15,193 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0267.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:80000001-81195210 -L 18:1-10000000 INFO 12:21:15,193 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-690.out INFO 12:21:30,072 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0268.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:10000001-20000000 INFO 12:21:30,072 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-692.out INFO 12:21:43,464 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0269.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:20000001-30000000 INFO 12:21:43,464 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-694.out INFO 12:21:57,661 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0270.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:30000001-40000000 INFO 12:21:57,661 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-696.out INFO 12:22:12,465 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0271.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:40000001-50000000 INFO 12:22:12,465 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-698.out INFO 12:22:28,171 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0272.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:50000001-60000000 INFO 12:22:28,171 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-700.out INFO 12:22:42,241 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0273.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:60000001-70000000 INFO 12:22:42,241 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-702.out INFO 12:22:56,603 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0274.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:70000001-78077248 -L 20:1-10000000 INFO 12:22:56,603 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-704.out INFO 12:23:18,951 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0275.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 20:10000001-20000000 INFO 12:23:18,951 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-706.out INFO 12:23:32,808 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0276.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 20:20000001-30000000 INFO 12:23:32,808 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-708.out INFO 12:23:46,887 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0277.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 20:30000001-40000000 INFO 12:23:46,888 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-710.out INFO 12:24:01,110 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0278.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 20:40000001-50000000 INFO 12:24:01,110 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-712.out INFO 12:24:15,287 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0279.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 20:50000001-60000000 INFO 12:24:15,287 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-714.out INFO 12:24:33,695 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0280.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 20:60000001-63025520 -L Y:1-10000000 INFO 12:24:33,695 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-716.out INFO 12:24:51,303 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0281.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L Y:10000001-20000000 INFO 12:24:51,303 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-718.out INFO 12:25:05,326 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0282.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L Y:20000001-30000000 INFO 12:25:05,326 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-720.out INFO 12:25:19,521 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0283.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L Y:30000001-40000000 INFO 12:25:19,521 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-722.out INFO 12:25:33,977 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0284.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L Y:40000001-50000000 INFO 12:25:33,977 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-724.out INFO 12:25:49,875 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0285.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L Y:50000001-59373566 -L 19:1-10000000 INFO 12:25:49,875 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-726.out INFO 12:26:13,964 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0286.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 19:10000001-20000000 INFO 12:26:13,964 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-728.out INFO 12:26:30,687 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0287.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 19:20000001-30000000 INFO 12:26:30,687 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-730.out INFO 12:26:44,255 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0288.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 19:30000001-40000000 INFO 12:26:44,255 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-732.out INFO 12:26:58,407 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0289.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 19:40000001-50000000 INFO 12:26:58,407 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-734.out INFO 12:27:13,123 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0290.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 19:50000001-59128983 -L 22:1-10000000 INFO 12:27:13,123 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-736.out INFO 12:27:36,854 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0291.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 22:10000001-20000000 INFO 12:27:36,854 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-738.out INFO 12:27:53,612 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0292.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 22:20000001-30000000 INFO 12:27:53,612 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-740.out INFO 12:28:07,986 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0293.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 22:30000001-40000000 INFO 12:28:07,986 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-742.out INFO 12:28:21,877 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0294.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 22:40000001-50000000 INFO 12:28:21,877 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-744.out INFO 12:28:39,555 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0295.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 22:50000001-51304566 -L 21:1-10000000 INFO 12:28:39,555 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-746.out INFO 12:28:54,652 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0296.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 21:10000001-20000000 INFO 12:28:54,652 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-748.out INFO 12:29:08,737 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0297.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 21:20000001-30000000 INFO 12:29:08,737 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-750.out INFO 12:29:26,688 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0298.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 21:30000001-40000000 INFO 12:29:26,688 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-752.out INFO 12:29:41,317 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0299.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 21:40000001-48129895 -L GL000192.1:1-547496 -L GL000225.1:1-211173 -L GL000194.1:1-191469 -L GL000193.1:1-189789 -L GL000200.1:1-187035 -L GL000222.1:1-186861 -L GL000212.1:1-186858 -L GL000195.1:1-182896 INFO 12:29:41,317 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-754.out INFO 12:29:55,735 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0300.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L GL000223.1:1-180455 -L GL000224.1:1-179693 -L GL000219.1:1-179198 -L GL000205.1:1-174588 -L GL000215.1:1-172545 -L GL000216.1:1-172294 -L GL000217.1:1-172149 -L NC_007605:1-171823 -L GL000199.1:1-169874 -L GL000211.1:1-166566 -L GL000213.1:1-164239 -L GL000220.1:1-161802 -L GL000218.1:1-161147 -L GL000209.1:1-159169 -L GL000221.1:1-155397 -L GL000214.1:1-137718 -L GL000228.1:1-129120 -L GL000227.1:1-128374 -L GL000191.1:1-106433 -L GL000208.1:1-92689 -L GL000198.1:1-90085 -L GL000204.1:1-81310 -L GL000233.1:1-45941 -L GL000237.1:1-45867 -L GL000230.1:1-43691 -L GL000242.1:1-43523 -L GL000243.1:1-43341 -L GL000241.1:1-42152 -L GL000236.1:1-41934 -L GL000240.1:1-41933 -L GL000206.1:1-41001 -L GL000232.1:1-40652 -L GL000234.1:1-40531 -L GL000202.1:1-40103 -L GL000238.1:1-39939 -L GL000244.1:1-39929 -L GL000248.1:1-39786 -L GL000196.1:1-38914 -L GL000249.1:1-38502 -L GL000246.1:1-38154 -L GL000203.1:1-37498 -L GL000197.1:1-37175 -L GL000245.1:1-36651 -L GL000247.1:1-36422 -L GL000201.1:1-36148 -L GL000235.1:1-34474 -L GL000239.1:1-33824 -L GL000210.1:1-27682 -L GL000231.1:1-27386 -L GL000229.1:1-19913 -L MT:1-16569 -L GL000226.1:1-15008 -L GL000207.1:1-4262 INFO 12:29:55,735 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-756.out INFO 12:30:05,168 QGraph - 477 Pend, 300 Run, 3 Fail, 153 Done INFO 12:30:05,172 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0168.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:20000001-30000000 INFO 12:30:05,172 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0216.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:100000001-110000000 INFO 12:30:05,172 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0212.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:60000001-70000000 INFO 12:30:05,178 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0260.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:10000001-20000000 INFO 12:30:05,181 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0124.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:20000001-30000000 INFO 12:30:05,181 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0239.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:90000001-100000000 INFO 12:30:05,181 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0283.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L Y:30000001-40000000 INFO 12:30:05,181 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0080.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:120000001-130000000 INFO 12:30:05,182 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0031.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:60000001-70000000 INFO 12:30:05,182 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0045.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:200000001-210000000 INFO 12:30:05,182 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0114.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:90000001-100000000 INFO 12:30:05,182 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0202.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:90000001-100000000 INFO 12:30:05,183 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0089.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:20000001-30000000 INFO 12:30:05,183 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0041.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:160000001-170000000 INFO 12:30:05,183 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0230.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:110000001-115169878 -L 14:1-10000000 INFO 12:30:05,183 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0054.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:50000001-60000000 INFO 12:30:05,183 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0109.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:40000001-50000000 INFO 12:30:05,184 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0028.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:30000001-40000000 INFO 12:30:05,189 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0142.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:50000001-60000000 INFO 12:30:05,189 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0175.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:90000001-100000000 INFO 12:30:05,189 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0225.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:60000001-70000000 INFO 12:30:05,190 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0050.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:10000001-20000000 INFO 12:30:05,190 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0278.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 20:40000001-50000000 INFO 12:30:05,190 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0094.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:70000001-80000000 INFO 12:30:05,190 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0147.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:100000001-110000000 INFO 12:30:05,190 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0170.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:40000001-50000000 INFO 12:30:05,191 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0285.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L Y:50000001-59373566 -L 19:1-10000000 INFO 12:30:05,191 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0107.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:20000001-30000000 INFO 12:30:05,191 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0151.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:140000001-150000000 INFO 12:30:05,191 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0195.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:20000001-30000000 INFO 12:30:05,191 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0059.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:100000001-110000000 INFO 12:30:05,192 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0016.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:150000001-160000000 INFO 12:30:05,192 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0280.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 20:60000001-63025520 -L Y:1-10000000 INFO 12:30:05,192 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0112.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:70000001-80000000 INFO 12:30:05,192 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0292.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 22:20000001-30000000 INFO 12:30:05,192 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0077.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:90000001-100000000 INFO 12:30:05,192 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0150.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:130000001-140000000 INFO 12:30:05,193 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0121.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:160000001-170000000 INFO 12:30:05,193 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0138.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:10000001-20000000 INFO 12:30:05,193 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0297.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 21:20000001-30000000 INFO 12:30:05,193 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0182.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:20000001-30000000 INFO 12:30:05,193 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0248.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:80000001-90000000 INFO 12:30:05,194 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0187.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:70000001-80000000 INFO 12:30:05,194 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0024.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:230000001-240000000 INFO 12:30:05,194 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0143.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:60000001-70000000 INFO 12:30:05,194 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0057.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:80000001-90000000 INFO 12:30:05,194 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0155.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:30000001-40000000 INFO 12:30:05,195 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0233.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:30000001-40000000 INFO 12:30:05,195 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0253.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:30000001-40000000 INFO 12:30:05,195 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0011.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:100000001-110000000 INFO 12:30:05,195 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0020.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:190000001-200000000 INFO 12:30:05,195 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0029.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:40000001-50000000 INFO 12:30:05,196 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0086.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:180000001-190000000 INFO 12:30:05,196 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0042.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:170000001-180000000 INFO 12:30:05,196 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0183.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:30000001-40000000 INFO 12:30:05,196 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0062.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:130000001-140000000 INFO 12:30:05,196 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0265.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:60000001-70000000 INFO 12:30:05,197 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0221.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:20000001-30000000 INFO 12:30:05,197 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0126.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:40000001-50000000 INFO 12:30:05,197 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0003.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:20000001-30000000 INFO 12:30:05,197 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0082.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:140000001-150000000 INFO 12:30:05,197 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0163.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:110000001-120000000 INFO 12:30:05,198 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0228.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:90000001-100000000 INFO 12:30:05,198 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0200.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:70000001-80000000 INFO 12:30:05,198 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0271.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:40000001-50000000 INFO 12:30:05,198 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0017.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:160000001-170000000 INFO 12:30:05,198 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0047.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:220000001-230000000 INFO 12:30:05,199 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0091.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:40000001-50000000 INFO 12:30:05,199 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0135.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:130000001-140000000 INFO 12:30:05,199 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0179.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:130000001-140000000 INFO 12:30:05,199 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0255.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:50000001-60000000 INFO 12:30:05,199 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0223.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:40000001-50000000 INFO 12:30:05,200 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0174.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:80000001-90000000 INFO 12:30:05,200 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0211.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:50000001-60000000 INFO 12:30:05,200 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0130.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:80000001-90000000 INFO 12:30:05,200 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0218.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:120000001-130000000 INFO 12:30:05,201 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0188.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:80000001-90000000 INFO 12:30:05,201 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0289.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 19:40000001-50000000 INFO 12:30:05,201 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0245.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:50000001-60000000 INFO 12:30:05,202 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0158.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:60000001-70000000 INFO 12:30:05,202 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0262.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:30000001-40000000 INFO 12:30:05,202 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0070.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:20000001-30000000 INFO 12:30:05,203 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0144.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:70000001-80000000 INFO 12:30:05,203 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0012.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:110000001-120000000 INFO 12:30:05,203 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0176.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:100000001-110000000 INFO 12:30:05,203 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0153.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:10000001-20000000 INFO 12:30:05,204 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0032.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:70000001-80000000 INFO 12:30:05,204 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0079.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:110000001-120000000 INFO 12:30:05,204 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0065.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:160000001-170000000 INFO 12:30:05,204 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0167.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:10000001-20000000 INFO 12:30:05,205 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0257.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:70000001-80000000 INFO 12:30:05,205 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0035.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:100000001-110000000 INFO 12:30:05,205 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0274.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:70000001-78077248 -L 20:1-10000000 INFO 12:30:05,205 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0213.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:70000001-80000000 INFO 12:30:05,205 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0123.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:10000001-20000000 INFO 12:30:05,206 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0098.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:110000001-120000000 INFO 12:30:05,206 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0269.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:20000001-30000000 INFO 12:30:05,206 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0208.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:20000001-30000000 INFO 12:30:05,206 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0118.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:130000001-140000000 INFO 12:30:05,207 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0103.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:160000001-170000000 INFO 12:30:05,207 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0282.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L Y:20000001-30000000 INFO 12:30:05,207 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0162.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:100000001-110000000 INFO 12:30:05,208 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0294.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 22:40000001-50000000 INFO 12:30:05,208 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0241.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:10000001-20000000 INFO 12:30:05,209 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0005.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:40000001-50000000 INFO 12:30:05,209 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0236.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:60000001-70000000 INFO 12:30:05,209 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0206.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:130000001-135006516 -L 12:1-10000000 INFO 12:30:05,210 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0250.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:100000001-102531392 -L 16:1-10000000 INFO 12:30:05,210 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0074.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:60000001-70000000 INFO 12:30:05,210 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0037.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:120000001-130000000 INFO 12:30:05,211 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0171.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:50000001-60000000 INFO 12:30:05,211 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0229.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:100000001-110000000 INFO 12:30:05,211 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0046.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:210000001-220000000 INFO 12:30:05,212 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0083.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:150000001-160000000 INFO 12:30:05,212 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0273.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:60000001-70000000 INFO 12:30:05,212 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0097.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:100000001-110000000 INFO 12:30:05,213 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0217.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:110000001-120000000 INFO 12:30:05,213 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0194.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:10000001-20000000 INFO 12:30:05,213 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0053.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:40000001-50000000 INFO 12:30:05,214 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0106.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:10000001-20000000 INFO 12:30:05,214 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0078.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:100000001-110000000 INFO 12:30:05,214 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0242.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:20000001-30000000 INFO 12:30:05,215 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0203.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:100000001-110000000 INFO 12:30:05,215 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0237.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:70000001-80000000 INFO 12:30:05,215 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0199.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:60000001-70000000 INFO 12:30:05,216 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0254.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:40000001-50000000 INFO 12:30:05,216 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0287.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 19:20000001-30000000 INFO 12:30:05,216 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0281.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L Y:10000001-20000000 INFO 12:30:05,216 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0268.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:10000001-20000000 INFO 12:30:05,217 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0224.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:50000001-60000000 INFO 12:30:05,217 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0023.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:220000001-230000000 INFO 12:30:05,217 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0111.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:60000001-70000000 INFO 12:30:05,217 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0286.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 19:10000001-20000000 INFO 12:30:05,218 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0139.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:20000001-30000000 INFO 12:30:05,218 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0040.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:150000001-160000000 INFO 12:30:05,218 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0051.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:20000001-30000000 INFO 12:30:05,219 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0222.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:30000001-40000000 INFO 12:30:05,219 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0066.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:170000001-180000000 INFO 12:30:05,219 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0110.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:50000001-60000000 INFO 12:30:05,220 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0249.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:90000001-100000000 INFO 12:30:05,220 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0008.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:70000001-80000000 INFO 12:30:05,220 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0014.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:130000001-140000000 INFO 12:30:05,221 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0277.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 20:30000001-40000000 INFO 12:30:05,221 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0295.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 22:50000001-51304566 -L 21:1-10000000 INFO 12:30:05,221 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0156.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:40000001-50000000 INFO 12:30:05,222 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0119.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:140000001-150000000 INFO 12:30:05,222 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0115.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:100000001-110000000 INFO 12:30:05,222 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0071.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:30000001-40000000 INFO 12:30:05,223 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0058.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:90000001-100000000 INFO 12:30:05,223 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0172.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:60000001-70000000 INFO 12:30:05,223 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0102.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:150000001-160000000 INFO 12:30:05,224 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0128.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:60000001-70000000 INFO 12:30:05,224 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0146.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:90000001-100000000 INFO 12:30:05,224 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0063.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:140000001-150000000 INFO 12:30:05,225 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0190.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:100000001-110000000 INFO 12:30:05,225 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0001.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:1-10000000 INFO 12:30:05,225 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0019.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:180000001-190000000 INFO 12:30:05,225 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0133.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:110000001-120000000 INFO 12:30:05,226 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0026.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:10000001-20000000 INFO 12:30:05,226 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0234.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:40000001-50000000 INFO 12:30:05,226 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0177.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:110000001-120000000 INFO 12:30:05,226 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0290.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 19:50000001-59128983 -L 22:1-10000000 INFO 12:30:05,227 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0197.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:40000001-50000000 INFO 12:30:05,227 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0072.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:40000001-50000000 INFO 12:30:05,227 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0006.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:50000001-60000000 INFO 12:30:05,228 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0298.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 21:30000001-40000000 INFO 12:30:05,228 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0132.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:100000001-110000000 INFO 12:30:05,228 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0243.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:30000001-40000000 INFO 12:30:05,229 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0220.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:10000001-20000000 INFO 12:30:05,229 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0116.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:110000001-120000000 INFO 12:30:05,229 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0021.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:200000001-210000000 INFO 12:30:05,230 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0252.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:20000001-30000000 INFO 12:30:05,230 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0164.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:120000001-130000000 INFO 12:30:05,230 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0087.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:190000001-191154276 -L 5:1-10000000 INFO 12:30:05,231 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0076.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:80000001-90000000 INFO 12:30:05,231 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0141.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:40000001-50000000 INFO 12:30:05,231 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0081.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:130000001-140000000 INFO 12:30:05,232 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0049.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:240000001-243199373 -L 3:1-10000000 INFO 12:30:05,232 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0137.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:150000001-159138663 -L X:1-10000000 INFO 12:30:05,232 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0258.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:80000001-90000000 ERROR 12:30:05,233 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0104.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:170000001-180000000 ERROR 12:30:05,233 FunctionEdge - Contents of /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-364.out: INFO 11:41:18,788 HelpFormatter - -------------------------------------------------------- INFO 11:41:18,790 HelpFormatter - Program Name: org.broadinstitute.sv.apps.MergeReadCounts INFO 11:41:18,793 HelpFormatter - Program Args: -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list -O /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0104.rccache.bin -R /work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta -L 5:170000001-180000000 INFO 11:41:18,794 HelpFormatter - Executing as wsh@localhost on Linux 2.6.32-696.6.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_141-b15. INFO 11:41:18,795 HelpFormatter - Date/Time: 2018/02/01 11:41:18 INFO 11:41:18,795 HelpFormatter - -------------------------------------------------------- INFO 11:41:18,795 HelpFormatter - -------------------------------------------------------- INFO 11:41:28,775 CommandLineProgram - Program completed. ------------------------------------------------------------------------------------------ Done. There were no warn messages. ------------------------------------------------------------------------------------------ INFO 12:30:05,234 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0044.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:190000001-200000000 INFO 12:30:05,234 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0169.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:30000001-40000000 INFO 12:30:05,234 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0192.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:120000001-130000000 INFO 12:30:05,235 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0127.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:50000001-60000000 INFO 12:30:05,235 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0185.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:50000001-60000000 INFO 12:30:05,235 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0263.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:40000001-50000000 INFO 12:30:05,235 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0099.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:120000001-130000000 INFO 12:30:05,236 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0261.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:20000001-30000000 INFO 12:30:05,236 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0270.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:30000001-40000000 INFO 12:30:05,236 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0275.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 20:10000001-20000000 INFO 12:30:05,237 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0226.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:70000001-80000000 INFO 12:30:05,237 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0160.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:80000001-90000000 INFO 12:30:05,237 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0165.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:130000001-140000000 INFO 12:30:05,238 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0209.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:30000001-40000000 INFO 12:30:05,238 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0002.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:10000001-20000000 INFO 12:30:05,238 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0204.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:110000001-120000000 INFO 12:30:05,239 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0238.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:80000001-90000000 INFO 12:30:05,239 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0039.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:140000001-150000000 INFO 12:30:05,239 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0178.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:120000001-130000000 INFO 12:30:05,240 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0090.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:30000001-40000000 INFO 12:30:05,240 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0034.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:90000001-100000000 INFO 12:30:05,240 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0067.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:180000001-190000000 INFO 12:30:05,241 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0033.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:80000001-90000000 INFO 12:30:05,241 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0231.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:10000001-20000000 INFO 12:30:05,242 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0210.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:40000001-50000000 INFO 12:30:05,242 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0122.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:170000001-171115067 -L 7:1-10000000 INFO 12:30:05,242 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0055.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:60000001-70000000 INFO 12:30:05,243 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0145.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:80000001-90000000 INFO 12:30:05,243 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0108.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:30000001-40000000 INFO 12:30:05,243 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0205.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:120000001-130000000 INFO 12:30:05,243 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0064.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:150000001-160000000 INFO 12:30:05,244 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0084.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:160000001-170000000 INFO 12:30:05,244 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0256.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:60000001-70000000 INFO 12:30:05,244 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0279.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 20:50000001-60000000 INFO 12:30:05,244 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0288.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 19:30000001-40000000 INFO 12:30:05,245 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0117.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:120000001-130000000 INFO 12:30:05,245 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0293.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 22:30000001-40000000 INFO 12:30:05,245 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0007.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:60000001-70000000 INFO 12:30:05,245 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0095.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:80000001-90000000 INFO 12:30:05,245 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0266.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:70000001-80000000 INFO 12:30:05,246 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0038.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:130000001-140000000 INFO 12:30:05,246 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0025.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:240000001-249250621 -L 2:1-10000000 INFO 12:30:05,246 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0140.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:30000001-40000000 INFO 12:30:05,246 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0299.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 21:40000001-48129895 -L GL000192.1:1-547496 -L GL000225.1:1-211173 -L GL000194.1:1-191469 -L GL000193.1:1-189789 -L GL000200.1:1-187035 -L GL000222.1:1-186861 -L GL000212.1:1-186858 -L GL000195.1:1-182896 INFO 12:30:05,246 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0085.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:170000001-180000000 INFO 12:30:05,247 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0052.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:30000001-40000000 INFO 12:30:05,247 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0173.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:70000001-80000000 INFO 12:30:05,247 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0105.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:180000001-180915260 -L 6:1-10000000 INFO 12:30:05,247 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0251.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:10000001-20000000 INFO 12:30:05,247 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0075.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:70000001-80000000 INFO 12:30:05,248 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0113.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:80000001-90000000 INFO 12:30:05,248 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0061.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:120000001-130000000 INFO 12:30:05,248 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0069.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:10000001-20000000 INFO 12:30:05,248 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0157.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:50000001-60000000 INFO 12:30:05,248 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0284.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L Y:40000001-50000000 INFO 12:30:05,249 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0201.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:80000001-90000000 INFO 12:30:05,249 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0232.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:20000001-30000000 INFO 12:30:05,249 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0264.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:50000001-60000000 INFO 12:30:05,249 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0056.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:70000001-80000000 INFO 12:30:05,249 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0181.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:10000001-20000000 INFO 12:30:05,250 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0196.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:30000001-40000000 INFO 12:30:05,250 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0100.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:130000001-140000000 INFO 12:30:05,250 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0276.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 20:20000001-30000000 INFO 12:30:05,250 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0246.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:60000001-70000000 INFO 12:30:05,250 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0267.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 17:80000001-81195210 -L 18:1-10000000 INFO 12:30:05,251 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0152.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:150000001-155270560 -L 8:1-10000000 INFO 12:30:05,251 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0240.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:100000001-107349540 -L 15:1-10000000 INFO 12:30:05,251 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0296.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 21:10000001-20000000 INFO 12:30:05,251 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0191.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:110000001-120000000 INFO 12:30:05,251 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0043.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:180000001-190000000 INFO 12:30:05,252 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0120.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 6:150000001-160000000 INFO 12:30:05,252 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0186.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:60000001-70000000 INFO 12:30:05,252 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0088.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:10000001-20000000 INFO 12:30:05,252 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0010.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:90000001-100000000 INFO 12:30:05,252 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0131.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:90000001-100000000 INFO 12:30:05,253 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0214.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:80000001-90000000 INFO 12:30:05,253 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0060.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:110000001-120000000 INFO 12:30:05,253 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0015.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:140000001-150000000 INFO 12:30:05,253 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0093.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:60000001-70000000 INFO 12:30:05,253 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0030.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:50000001-60000000 INFO 12:30:05,254 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0125.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:30000001-40000000 INFO 12:30:05,254 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0148.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:110000001-120000000 INFO 12:30:05,254 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0219.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:130000001-133851895 -L 13:1-10000000 INFO 12:30:05,254 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0193.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:130000001-135534747 -L 11:1-10000000 INFO 12:30:05,254 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0149.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L X:120000001-130000000 INFO 12:30:05,255 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0134.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:120000001-130000000 INFO 12:30:05,255 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0159.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:70000001-80000000 INFO 12:30:05,255 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0092.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:50000001-60000000 INFO 12:30:05,255 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0215.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:90000001-100000000 INFO 12:30:05,255 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0300.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L GL000223.1:1-180455 -L GL000224.1:1-179693 -L GL000219.1:1-179198 -L GL000205.1:1-174588 -L GL000215.1:1-172545 -L GL000216.1:1-172294 -L GL000217.1:1-172149 -L NC_007605:1-171823 -L GL000199.1:1-169874 -L GL000211.1:1-166566 -L GL000213.1:1-164239 -L GL000220.1:1-161802 -L GL000218.1:1-161147 -L GL000209.1:1-159169 -L GL000221.1:1-155397 -L GL000214.1:1-137718 -L GL000228.1:1-129120 -L GL000227.1:1-128374 -L GL000191.1:1-106433 -L GL000208.1:1-92689 -L GL000198.1:1-90085 -L GL000204.1:1-81310 -L GL000233.1:1-45941 -L GL000237.1:1-45867 -L GL000230.1:1-43691 -L GL000242.1:1-43523 -L GL000243.1:1-43341 -L GL000241.1:1-42152 -L GL000236.1:1-41934 -L GL000240.1:1-41933 -L GL000206.1:1-41001 -L GL000232.1:1-40652 -L GL000234.1:1-40531 -L GL000202.1:1-40103 -L GL000238.1:1-39939 -L GL000244.1:1-39929 -L GL000248.1:1-39786 -L GL000196.1:1-38914 -L GL000249.1:1-38502 -L GL000246.1:1-38154 -L GL000203.1:1-37498 -L GL000197.1:1-37175 -L GL000245.1:1-36651 -L GL000247.1:1-36422 -L GL000201.1:1-36148 -L GL000235.1:1-34474 -L GL000239.1:1-33824 -L GL000210.1:1-27682 -L GL000231.1:1-27386 -L GL000229.1:1-19913 -L MT:1-16569 -L GL000226.1:1-15008 -L GL000207.1:1-4262 INFO 12:30:05,256 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0004.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:30000001-40000000 INFO 12:30:05,256 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0048.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:230000001-240000000 INFO 12:30:05,256 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0259.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 16:90000001-90354753 -L 17:1-10000000 INFO 12:30:05,256 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0189.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:90000001-100000000 INFO 12:30:05,256 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0136.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:140000001-150000000 INFO 12:30:05,257 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0166.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:140000001-146364022 -L 9:1-10000000 INFO 12:30:05,257 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0180.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 9:140000001-141213431 -L 10:1-10000000 INFO 12:30:05,257 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0009.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:80000001-90000000 INFO 12:30:05,257 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0235.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 14:50000001-60000000 INFO 12:30:05,257 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0247.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:70000001-80000000 INFO 12:30:05,258 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0291.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 22:10000001-20000000 INFO 12:30:05,258 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0013.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:120000001-130000000 INFO 12:30:05,258 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0154.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:20000001-30000000 INFO 12:30:05,258 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0198.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 11:50000001-60000000 INFO 12:30:05,259 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0101.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:140000001-150000000 INFO 12:30:05,259 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0018.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:170000001-180000000 INFO 12:30:05,259 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0161.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 8:90000001-100000000 INFO 12:30:05,259 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0244.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 15:40000001-50000000 INFO 12:30:05,259 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0073.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 4:50000001-60000000 INFO 12:30:05,260 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0027.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:20000001-30000000 INFO 12:30:05,260 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0184.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 10:40000001-50000000 INFO 12:30:05,260 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0207.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 12:10000001-20000000 INFO 12:30:05,260 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0129.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 7:70000001-80000000 INFO 12:30:05,261 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0096.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:90000001-100000000 INFO 12:30:05,261 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0272.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 18:50000001-60000000 INFO 12:30:05,261 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0068.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 3:190000001-198022430 -L 4:1-10000000 INFO 12:30:05,261 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0036.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 2:110000001-120000000 INFO 12:30:05,261 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0022.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 1:210000001-220000000 INFO 12:30:05,262 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0227.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 13:80000001-90000000 INFO 12:30:05,262 QGraph - Writing incremental jobs reports... INFO 12:30:05,273 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0001.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0001.rccache.bin.idx' INFO 12:30:05,273 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-159.out INFO 12:30:09,324 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0002.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0002.rccache.bin.idx' INFO 12:30:09,325 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-161.out INFO 12:30:13,299 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0003.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0003.rccache.bin.idx' INFO 12:30:13,299 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-163.out INFO 12:30:17,429 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0004.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0004.rccache.bin.idx' INFO 12:30:17,429 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-165.out INFO 12:30:24,153 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0005.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0005.rccache.bin.idx' INFO 12:30:24,153 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-167.out INFO 12:30:28,261 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0006.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0006.rccache.bin.idx' INFO 12:30:28,261 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-169.out INFO 12:30:32,309 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0007.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0007.rccache.bin.idx' INFO 12:30:32,309 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-171.out INFO 12:30:36,219 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0008.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0008.rccache.bin.idx' INFO 12:30:36,219 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-173.out INFO 12:30:40,267 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0009.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0009.rccache.bin.idx' INFO 12:30:40,267 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-175.out INFO 12:30:44,265 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0010.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0010.rccache.bin.idx' INFO 12:30:44,267 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-177.out INFO 12:30:48,294 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0011.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0011.rccache.bin.idx' INFO 12:30:48,294 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-179.out INFO 12:30:52,333 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0012.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0012.rccache.bin.idx' INFO 12:30:52,334 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-181.out INFO 12:30:56,239 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0013.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0013.rccache.bin.idx' INFO 12:30:56,239 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-183.out INFO 12:31:00,237 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0014.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0014.rccache.bin.idx' INFO 12:31:00,237 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-185.out INFO 12:31:04,455 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0015.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0015.rccache.bin.idx' INFO 12:31:04,455 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-187.out INFO 12:31:08,514 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0016.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0016.rccache.bin.idx' INFO 12:31:08,514 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-189.out INFO 12:31:12,578 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0017.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0017.rccache.bin.idx' INFO 12:31:12,578 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-191.out INFO 12:31:16,566 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0018.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0018.rccache.bin.idx' INFO 12:31:16,566 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-193.out INFO 12:31:20,573 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0019.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0019.rccache.bin.idx' INFO 12:31:20,573 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-195.out INFO 12:31:24,537 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0020.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0020.rccache.bin.idx' INFO 12:31:24,538 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-197.out INFO 12:31:28,515 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0021.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0021.rccache.bin.idx' INFO 12:31:28,515 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-199.out INFO 12:31:32,499 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0022.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0022.rccache.bin.idx' INFO 12:31:32,499 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-201.out INFO 12:31:36,548 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0023.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0023.rccache.bin.idx' INFO 12:31:36,548 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-203.out INFO 12:31:40,744 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0024.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0024.rccache.bin.idx' INFO 12:31:40,744 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-205.out INFO 12:31:44,719 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0025.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0025.rccache.bin.idx' INFO 12:31:44,719 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-207.out INFO 12:31:48,877 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0026.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0026.rccache.bin.idx' INFO 12:31:48,877 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-209.out INFO 12:31:52,820 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0027.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0027.rccache.bin.idx' INFO 12:31:52,820 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-211.out INFO 12:31:56,866 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0028.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0028.rccache.bin.idx' INFO 12:31:56,866 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-213.out INFO 12:32:00,907 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0029.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0029.rccache.bin.idx' INFO 12:32:00,908 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-215.out INFO 12:32:04,859 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0030.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0030.rccache.bin.idx' INFO 12:32:04,859 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-217.out INFO 12:32:08,936 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0031.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0031.rccache.bin.idx' INFO 12:32:08,936 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-219.out INFO 12:32:13,000 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0032.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0032.rccache.bin.idx' INFO 12:32:13,000 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-221.out INFO 12:32:16,990 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0033.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0033.rccache.bin.idx' INFO 12:32:16,990 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-223.out INFO 12:32:21,006 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0034.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0034.rccache.bin.idx' INFO 12:32:21,006 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-225.out INFO 12:32:26,529 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0035.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0035.rccache.bin.idx' INFO 12:32:26,529 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-227.out INFO 12:32:30,864 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0036.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0036.rccache.bin.idx' INFO 12:32:30,864 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-229.out INFO 12:32:34,862 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0037.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0037.rccache.bin.idx' INFO 12:32:34,862 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-231.out INFO 12:32:38,813 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0038.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0038.rccache.bin.idx' INFO 12:32:38,813 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-233.out INFO 12:32:42,862 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0039.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0039.rccache.bin.idx' INFO 12:32:42,862 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-235.out INFO 12:32:46,869 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0040.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0040.rccache.bin.idx' INFO 12:32:46,869 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-237.out INFO 12:32:51,004 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0041.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0041.rccache.bin.idx' INFO 12:32:51,004 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-239.out INFO 12:32:55,109 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0042.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0042.rccache.bin.idx' INFO 12:32:55,109 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-241.out INFO 12:32:59,298 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0043.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0043.rccache.bin.idx' INFO 12:32:59,298 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-243.out INFO 12:33:03,311 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0044.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0044.rccache.bin.idx' INFO 12:33:03,311 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-245.out INFO 12:33:07,362 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0045.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0045.rccache.bin.idx' INFO 12:33:07,362 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-247.out INFO 12:33:11,315 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0046.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0046.rccache.bin.idx' INFO 12:33:11,315 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-249.out INFO 12:33:15,314 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0047.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0047.rccache.bin.idx' INFO 12:33:15,315 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-251.out INFO 12:33:19,254 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0048.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0048.rccache.bin.idx' INFO 12:33:19,254 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-253.out INFO 12:33:23,299 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0049.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0049.rccache.bin.idx' INFO 12:33:23,299 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-255.out INFO 12:33:27,300 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0050.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0050.rccache.bin.idx' INFO 12:33:27,300 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-257.out INFO 12:33:31,289 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0051.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0051.rccache.bin.idx' INFO 12:33:31,289 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-259.out INFO 12:33:35,307 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0052.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0052.rccache.bin.idx' INFO 12:33:35,307 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-261.out INFO 12:33:39,433 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0053.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0053.rccache.bin.idx' INFO 12:33:39,433 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-263.out INFO 12:33:43,396 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0054.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0054.rccache.bin.idx' INFO 12:33:43,396 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-265.out INFO 12:33:47,402 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0055.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0055.rccache.bin.idx' INFO 12:33:47,402 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-267.out INFO 12:33:51,386 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0056.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0056.rccache.bin.idx' INFO 12:33:51,386 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-269.out INFO 12:33:55,427 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0057.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0057.rccache.bin.idx' INFO 12:33:55,427 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-271.out INFO 12:33:59,424 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0058.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0058.rccache.bin.idx' INFO 12:33:59,425 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-273.out INFO 12:34:03,414 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0059.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0059.rccache.bin.idx' INFO 12:34:03,414 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-275.out INFO 12:34:07,373 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0060.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0060.rccache.bin.idx' INFO 12:34:07,373 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-277.out INFO 12:34:11,445 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0061.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0061.rccache.bin.idx' INFO 12:34:11,445 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-279.out INFO 12:34:15,566 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0062.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0062.rccache.bin.idx' INFO 12:34:15,566 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-281.out INFO 12:34:19,625 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0063.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0063.rccache.bin.idx' INFO 12:34:19,625 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-283.out INFO 12:34:25,527 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0064.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0064.rccache.bin.idx' INFO 12:34:25,527 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-285.out INFO 12:34:29,666 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0065.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0065.rccache.bin.idx' INFO 12:34:29,666 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-287.out INFO 12:34:33,774 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0066.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0066.rccache.bin.idx' INFO 12:34:33,774 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-289.out INFO 12:34:37,848 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0067.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0067.rccache.bin.idx' INFO 12:34:37,848 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-291.out INFO 12:34:41,917 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0068.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0068.rccache.bin.idx' INFO 12:34:41,917 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-293.out INFO 12:34:46,091 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0069.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0069.rccache.bin.idx' INFO 12:34:46,091 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-295.out INFO 12:34:50,422 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0070.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0070.rccache.bin.idx' INFO 12:34:50,422 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-297.out INFO 12:34:54,528 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0071.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0071.rccache.bin.idx' INFO 12:34:54,528 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-299.out INFO 12:34:58,890 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0072.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0072.rccache.bin.idx' INFO 12:34:58,890 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-301.out INFO 12:35:02,847 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0073.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0073.rccache.bin.idx' INFO 12:35:02,847 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-303.out INFO 12:35:06,826 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0074.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0074.rccache.bin.idx' INFO 12:35:06,826 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-305.out INFO 12:35:10,879 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0075.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0075.rccache.bin.idx' INFO 12:35:10,879 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-307.out INFO 12:35:14,866 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0076.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0076.rccache.bin.idx' INFO 12:35:14,866 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-309.out INFO 12:35:18,989 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0077.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0077.rccache.bin.idx' INFO 12:35:18,990 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-311.out INFO 12:35:23,225 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0078.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0078.rccache.bin.idx' INFO 12:35:23,225 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-313.out INFO 12:35:27,362 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0079.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0079.rccache.bin.idx' INFO 12:35:27,362 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-315.out INFO 12:35:31,474 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0080.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0080.rccache.bin.idx' INFO 12:35:31,474 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-317.out INFO 12:35:35,575 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0081.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0081.rccache.bin.idx' INFO 12:35:35,575 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-319.out INFO 12:35:39,582 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0082.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0082.rccache.bin.idx' INFO 12:35:39,582 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-321.out INFO 12:35:43,649 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0083.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0083.rccache.bin.idx' INFO 12:35:43,649 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-323.out INFO 12:35:47,633 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0084.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0084.rccache.bin.idx' INFO 12:35:47,633 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-325.out INFO 12:35:51,680 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0085.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0085.rccache.bin.idx' INFO 12:35:51,680 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-327.out INFO 12:35:55,692 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0086.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0086.rccache.bin.idx' INFO 12:35:55,692 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-329.out INFO 12:35:59,752 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0087.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0087.rccache.bin.idx' INFO 12:35:59,752 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-331.out INFO 12:36:03,891 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0088.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0088.rccache.bin.idx' INFO 12:36:03,891 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-333.out INFO 12:36:07,904 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0089.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0089.rccache.bin.idx' INFO 12:36:07,904 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-335.out INFO 12:36:12,729 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0090.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0090.rccache.bin.idx' INFO 12:36:12,729 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-337.out INFO 12:36:16,730 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0091.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0091.rccache.bin.idx' INFO 12:36:16,730 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-339.out INFO 12:36:20,836 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0092.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0092.rccache.bin.idx' INFO 12:36:20,836 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-341.out INFO 12:36:24,817 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0093.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0093.rccache.bin.idx' INFO 12:36:24,817 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-343.out INFO 12:36:28,753 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0094.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0094.rccache.bin.idx' INFO 12:36:28,753 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-345.out INFO 12:36:32,678 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0095.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0095.rccache.bin.idx' INFO 12:36:32,678 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-347.out INFO 12:36:36,665 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0096.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0096.rccache.bin.idx' INFO 12:36:36,665 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-349.out INFO 12:36:40,757 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0097.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0097.rccache.bin.idx' INFO 12:36:40,757 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-351.out INFO 12:36:44,703 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0098.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0098.rccache.bin.idx' INFO 12:36:44,703 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-353.out INFO 12:36:48,688 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0099.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0099.rccache.bin.idx' INFO 12:36:48,688 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-355.out INFO 12:36:52,616 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0100.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0100.rccache.bin.idx' INFO 12:36:52,616 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-357.out INFO 12:36:56,514 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0101.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0101.rccache.bin.idx' INFO 12:36:56,514 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-359.out INFO 12:37:00,482 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0102.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0102.rccache.bin.idx' INFO 12:37:00,482 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-361.out INFO 12:37:04,397 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0103.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0103.rccache.bin.idx' INFO 12:37:04,398 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-363.out INFO 12:37:08,298 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0105.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0105.rccache.bin.idx' INFO 12:37:08,298 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-367.out INFO 12:37:12,215 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0106.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0106.rccache.bin.idx' INFO 12:37:12,215 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-369.out INFO 12:37:16,123 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0107.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0107.rccache.bin.idx' INFO 12:37:16,123 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-371.out INFO 12:37:20,217 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0108.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0108.rccache.bin.idx' INFO 12:37:20,218 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-373.out INFO 12:37:24,067 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0109.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0109.rccache.bin.idx' INFO 12:37:24,067 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-375.out INFO 12:37:28,134 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0110.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0110.rccache.bin.idx' INFO 12:37:28,135 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-377.out INFO 12:37:32,177 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0111.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0111.rccache.bin.idx' INFO 12:37:32,177 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-379.out INFO 12:37:36,215 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0112.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0112.rccache.bin.idx' INFO 12:37:36,215 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-381.out INFO 12:37:40,302 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0113.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0113.rccache.bin.idx' INFO 12:37:40,302 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-383.out INFO 12:37:44,378 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0114.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0114.rccache.bin.idx' INFO 12:37:44,378 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-385.out INFO 12:37:48,580 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0115.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0115.rccache.bin.idx' INFO 12:37:48,580 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-387.out INFO 12:37:52,706 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0116.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0116.rccache.bin.idx' INFO 12:37:52,706 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-389.out INFO 12:37:56,586 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0117.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0117.rccache.bin.idx' INFO 12:37:56,586 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-391.out INFO 12:38:00,530 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0118.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0118.rccache.bin.idx' INFO 12:38:00,530 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-393.out INFO 12:38:04,624 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0119.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0119.rccache.bin.idx' INFO 12:38:04,624 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-395.out INFO 12:38:10,433 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0120.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0120.rccache.bin.idx' INFO 12:38:10,433 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-397.out INFO 12:38:14,457 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0121.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0121.rccache.bin.idx' INFO 12:38:14,457 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-399.out INFO 12:38:18,504 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0122.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0122.rccache.bin.idx' INFO 12:38:18,504 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-401.out INFO 12:38:22,553 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0123.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0123.rccache.bin.idx' INFO 12:38:22,553 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-403.out INFO 12:38:26,604 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0124.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0124.rccache.bin.idx' INFO 12:38:26,604 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-405.out INFO 12:38:30,577 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0125.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0125.rccache.bin.idx' INFO 12:38:30,577 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-407.out INFO 12:38:34,598 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0126.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0126.rccache.bin.idx' INFO 12:38:34,598 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-409.out INFO 12:38:38,822 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0127.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0127.rccache.bin.idx' INFO 12:38:38,822 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-411.out INFO 12:38:42,886 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0128.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0128.rccache.bin.idx' INFO 12:38:42,886 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-413.out INFO 12:38:46,974 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0129.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0129.rccache.bin.idx' INFO 12:38:46,974 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-415.out INFO 12:38:50,878 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0130.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0130.rccache.bin.idx' INFO 12:38:50,878 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-417.out INFO 12:38:54,884 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0131.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0131.rccache.bin.idx' INFO 12:38:54,884 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-419.out INFO 12:38:59,040 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0132.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0132.rccache.bin.idx' INFO 12:38:59,040 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-421.out INFO 12:39:03,124 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0133.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0133.rccache.bin.idx' INFO 12:39:03,124 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-423.out INFO 12:39:07,192 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0134.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0134.rccache.bin.idx' INFO 12:39:07,193 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-425.out INFO 12:39:11,242 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0135.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0135.rccache.bin.idx' INFO 12:39:11,242 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-427.out INFO 12:39:15,404 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0136.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0136.rccache.bin.idx' INFO 12:39:15,404 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-429.out INFO 12:39:19,479 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0137.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0137.rccache.bin.idx' INFO 12:39:19,479 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-431.out INFO 12:39:23,751 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0138.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0138.rccache.bin.idx' INFO 12:39:23,751 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-433.out INFO 12:39:27,773 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0139.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0139.rccache.bin.idx' INFO 12:39:27,773 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-435.out INFO 12:39:31,807 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0140.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0140.rccache.bin.idx' INFO 12:39:31,807 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-437.out INFO 12:39:35,683 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0141.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0141.rccache.bin.idx' INFO 12:39:35,683 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-439.out INFO 12:39:39,564 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0142.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0142.rccache.bin.idx' INFO 12:39:39,564 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-441.out INFO 12:39:43,526 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0143.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0143.rccache.bin.idx' INFO 12:39:43,527 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-443.out INFO 12:39:47,524 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0144.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0144.rccache.bin.idx' INFO 12:39:47,524 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-445.out INFO 12:39:51,409 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0145.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0145.rccache.bin.idx' INFO 12:39:51,409 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-447.out INFO 12:39:55,312 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0146.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0146.rccache.bin.idx' INFO 12:39:55,312 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-449.out INFO 12:39:59,346 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0147.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0147.rccache.bin.idx' INFO 12:39:59,346 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-451.out INFO 12:40:03,440 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0148.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0148.rccache.bin.idx' INFO 12:40:03,440 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-453.out INFO 12:40:08,033 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0149.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0149.rccache.bin.idx' INFO 12:40:08,033 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-455.out INFO 12:40:13,182 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0150.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0150.rccache.bin.idx' INFO 12:40:13,182 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-457.out INFO 12:40:17,109 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0151.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0151.rccache.bin.idx' INFO 12:40:17,110 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-459.out INFO 12:40:21,119 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0152.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0152.rccache.bin.idx' INFO 12:40:21,119 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-461.out INFO 12:40:25,124 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0153.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0153.rccache.bin.idx' INFO 12:40:25,124 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-463.out INFO 12:40:29,118 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0154.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0154.rccache.bin.idx' INFO 12:40:29,118 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-465.out INFO 12:40:33,141 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0155.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0155.rccache.bin.idx' INFO 12:40:33,141 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-467.out INFO 12:40:38,413 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0156.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0156.rccache.bin.idx' INFO 12:40:38,413 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-469.out INFO 12:40:42,450 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0157.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0157.rccache.bin.idx' INFO 12:40:42,450 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-471.out INFO 12:40:46,708 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0158.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0158.rccache.bin.idx' INFO 12:40:46,708 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-473.out INFO 12:40:50,924 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0159.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0159.rccache.bin.idx' INFO 12:40:50,924 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-475.out INFO 12:40:54,904 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0160.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0160.rccache.bin.idx' INFO 12:40:54,904 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-477.out INFO 12:40:58,849 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0161.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0161.rccache.bin.idx' INFO 12:40:58,849 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-479.out INFO 12:41:02,771 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0162.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0162.rccache.bin.idx' INFO 12:41:02,771 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-481.out INFO 12:41:06,699 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0163.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0163.rccache.bin.idx' INFO 12:41:06,699 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-483.out INFO 12:41:10,566 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0164.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0164.rccache.bin.idx' INFO 12:41:10,567 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-485.out INFO 12:41:14,595 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0165.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0165.rccache.bin.idx' INFO 12:41:14,595 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-487.out INFO 12:41:18,704 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0166.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0166.rccache.bin.idx' INFO 12:41:18,704 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-489.out INFO 12:41:22,858 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0167.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0167.rccache.bin.idx' INFO 12:41:22,858 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-491.out INFO 12:41:26,872 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0168.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0168.rccache.bin.idx' INFO 12:41:26,873 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-493.out INFO 12:41:30,858 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0169.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0169.rccache.bin.idx' INFO 12:41:30,858 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-495.out INFO 12:41:34,826 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0170.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0170.rccache.bin.idx' INFO 12:41:34,826 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-497.out INFO 12:41:38,730 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0171.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0171.rccache.bin.idx' INFO 12:41:38,730 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-499.out INFO 12:41:42,704 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0172.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0172.rccache.bin.idx' INFO 12:41:42,704 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-501.out INFO 12:41:46,750 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0173.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0173.rccache.bin.idx' INFO 12:41:46,750 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-503.out INFO 12:41:50,664 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0174.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0174.rccache.bin.idx' INFO 12:41:50,665 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-505.out INFO 12:41:54,533 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0175.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0175.rccache.bin.idx' INFO 12:41:54,533 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-507.out INFO 12:41:58,479 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0176.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0176.rccache.bin.idx' INFO 12:41:58,479 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-509.out INFO 12:42:02,497 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0177.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0177.rccache.bin.idx' INFO 12:42:02,497 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-511.out INFO 12:42:07,892 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0178.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0178.rccache.bin.idx' INFO 12:42:07,892 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-513.out INFO 12:42:12,302 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0179.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0179.rccache.bin.idx' INFO 12:42:12,302 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-515.out INFO 12:42:16,268 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0180.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0180.rccache.bin.idx' INFO 12:42:16,268 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-517.out INFO 12:42:20,220 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0181.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0181.rccache.bin.idx' INFO 12:42:20,220 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-519.out INFO 12:42:24,372 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0182.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0182.rccache.bin.idx' INFO 12:42:24,373 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-521.out INFO 12:42:28,539 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0183.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0183.rccache.bin.idx' INFO 12:42:28,539 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-523.out INFO 12:42:32,540 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0184.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0184.rccache.bin.idx' INFO 12:42:32,540 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-525.out INFO 12:42:36,729 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0185.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0185.rccache.bin.idx' INFO 12:42:36,729 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-527.out INFO 12:42:40,643 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0186.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0186.rccache.bin.idx' INFO 12:42:40,643 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-529.out INFO 12:42:44,514 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0187.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0187.rccache.bin.idx' INFO 12:42:44,514 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-531.out INFO 12:42:48,407 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0188.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0188.rccache.bin.idx' INFO 12:42:48,407 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-533.out INFO 12:42:52,314 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0189.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0189.rccache.bin.idx' INFO 12:42:52,315 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-535.out INFO 12:42:56,215 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0190.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0190.rccache.bin.idx' INFO 12:42:56,215 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-537.out INFO 12:43:00,090 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0191.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0191.rccache.bin.idx' INFO 12:43:00,090 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-539.out INFO 12:43:04,173 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0192.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0192.rccache.bin.idx' INFO 12:43:04,173 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-541.out INFO 12:43:08,111 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0193.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0193.rccache.bin.idx' INFO 12:43:08,111 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-543.out INFO 12:43:12,171 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0194.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0194.rccache.bin.idx' INFO 12:43:12,171 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-545.out INFO 12:43:16,091 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0195.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0195.rccache.bin.idx' INFO 12:43:16,091 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-547.out INFO 12:43:20,075 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0196.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0196.rccache.bin.idx' INFO 12:43:20,075 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-549.out INFO 12:43:23,981 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0197.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0197.rccache.bin.idx' INFO 12:43:23,981 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-551.out INFO 12:43:27,976 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0198.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0198.rccache.bin.idx' INFO 12:43:27,976 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-553.out INFO 12:43:31,818 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0199.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0199.rccache.bin.idx' INFO 12:43:31,818 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-555.out INFO 12:43:35,849 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0200.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0200.rccache.bin.idx' INFO 12:43:35,849 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-557.out INFO 12:43:39,891 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0201.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0201.rccache.bin.idx' INFO 12:43:39,891 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-559.out INFO 12:43:43,896 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0202.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0202.rccache.bin.idx' INFO 12:43:43,896 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-561.out INFO 12:43:47,817 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0203.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0203.rccache.bin.idx' INFO 12:43:47,817 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-563.out INFO 12:43:51,890 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0204.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0204.rccache.bin.idx' INFO 12:43:51,890 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-565.out INFO 12:43:55,924 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0205.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0205.rccache.bin.idx' INFO 12:43:55,924 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-567.out INFO 12:44:00,059 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0206.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0206.rccache.bin.idx' INFO 12:44:00,060 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-569.out INFO 12:44:05,913 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0207.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0207.rccache.bin.idx' INFO 12:44:05,913 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-571.out INFO 12:44:10,831 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0208.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0208.rccache.bin.idx' INFO 12:44:10,831 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-573.out INFO 12:44:14,821 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0209.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0209.rccache.bin.idx' INFO 12:44:14,821 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-575.out INFO 12:44:18,870 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0210.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0210.rccache.bin.idx' INFO 12:44:18,870 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-577.out INFO 12:44:22,850 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0211.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0211.rccache.bin.idx' INFO 12:44:22,850 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-579.out INFO 12:44:26,760 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0212.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0212.rccache.bin.idx' INFO 12:44:26,760 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-581.out INFO 12:44:30,950 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0213.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0213.rccache.bin.idx' INFO 12:44:30,950 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-583.out INFO 12:44:34,979 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0214.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0214.rccache.bin.idx' INFO 12:44:34,979 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-585.out INFO 12:44:39,092 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0215.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0215.rccache.bin.idx' INFO 12:44:39,092 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-587.out INFO 12:44:43,043 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0216.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0216.rccache.bin.idx' INFO 12:44:43,043 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-589.out INFO 12:44:47,144 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0217.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0217.rccache.bin.idx' INFO 12:44:47,144 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-591.out INFO 12:44:51,063 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0218.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0218.rccache.bin.idx' INFO 12:44:51,063 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-593.out INFO 12:44:55,057 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0219.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0219.rccache.bin.idx' INFO 12:44:55,057 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-595.out INFO 12:44:59,079 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0220.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0220.rccache.bin.idx' INFO 12:44:59,079 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-597.out INFO 12:45:03,079 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0221.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0221.rccache.bin.idx' INFO 12:45:03,079 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-599.out INFO 12:45:07,119 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0222.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0222.rccache.bin.idx' INFO 12:45:07,119 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-601.out INFO 12:45:11,147 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0223.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0223.rccache.bin.idx' INFO 12:45:11,147 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-603.out INFO 12:45:15,174 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0224.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0224.rccache.bin.idx' INFO 12:45:15,174 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-605.out INFO 12:45:19,232 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0225.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0225.rccache.bin.idx' INFO 12:45:19,232 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-607.out INFO 12:45:23,219 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0226.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0226.rccache.bin.idx' INFO 12:45:23,219 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-609.out INFO 12:45:27,392 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0227.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0227.rccache.bin.idx' INFO 12:45:27,392 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-611.out INFO 12:45:31,431 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0228.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0228.rccache.bin.idx' INFO 12:45:31,431 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-613.out INFO 12:45:35,365 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0229.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0229.rccache.bin.idx' INFO 12:45:35,365 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-615.out INFO 12:45:39,466 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0230.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0230.rccache.bin.idx' INFO 12:45:39,466 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-617.out INFO 12:45:43,668 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0231.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0231.rccache.bin.idx' INFO 12:45:43,668 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-619.out INFO 12:45:47,578 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0232.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0232.rccache.bin.idx' INFO 12:45:47,578 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-621.out INFO 12:45:51,479 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0233.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0233.rccache.bin.idx' INFO 12:45:51,479 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-623.out INFO 12:45:55,576 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0234.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0234.rccache.bin.idx' INFO 12:45:55,576 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-625.out INFO 12:45:59,660 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0235.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0235.rccache.bin.idx' INFO 12:45:59,660 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-627.out INFO 12:46:06,059 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0236.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0236.rccache.bin.idx' INFO 12:46:06,059 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-629.out INFO 12:46:10,004 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0237.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0237.rccache.bin.idx' INFO 12:46:10,004 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-631.out INFO 12:46:14,043 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0238.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0238.rccache.bin.idx' INFO 12:46:14,043 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-633.out INFO 12:46:18,146 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0239.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0239.rccache.bin.idx' INFO 12:46:18,146 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-635.out INFO 12:46:22,115 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0240.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0240.rccache.bin.idx' INFO 12:46:22,116 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-637.out INFO 12:46:26,238 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0241.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0241.rccache.bin.idx' INFO 12:46:26,238 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-639.out INFO 12:46:30,240 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0242.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0242.rccache.bin.idx' INFO 12:46:30,240 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-641.out INFO 12:46:34,178 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0243.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0243.rccache.bin.idx' INFO 12:46:34,178 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-643.out INFO 12:46:38,195 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0244.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0244.rccache.bin.idx' INFO 12:46:38,195 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-645.out INFO 12:46:42,184 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0245.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0245.rccache.bin.idx' INFO 12:46:42,184 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-647.out INFO 12:46:46,257 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0246.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0246.rccache.bin.idx' INFO 12:46:46,257 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-649.out INFO 12:46:50,306 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0247.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0247.rccache.bin.idx' INFO 12:46:50,306 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-651.out INFO 12:46:54,322 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0248.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0248.rccache.bin.idx' INFO 12:46:54,322 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-653.out INFO 12:46:58,347 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0249.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0249.rccache.bin.idx' INFO 12:46:58,347 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-655.out INFO 12:47:02,375 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0250.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0250.rccache.bin.idx' INFO 12:47:02,375 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-657.out INFO 12:47:06,426 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0251.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0251.rccache.bin.idx' INFO 12:47:06,426 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-659.out INFO 12:47:10,419 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0252.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0252.rccache.bin.idx' INFO 12:47:10,419 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-661.out INFO 12:47:14,293 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0253.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0253.rccache.bin.idx' INFO 12:47:14,293 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-663.out INFO 12:47:18,275 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0254.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0254.rccache.bin.idx' INFO 12:47:18,275 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-665.out INFO 12:47:22,323 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0255.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0255.rccache.bin.idx' INFO 12:47:22,323 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-667.out INFO 12:47:26,332 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0256.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0256.rccache.bin.idx' INFO 12:47:26,332 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-669.out INFO 12:47:30,183 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0257.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0257.rccache.bin.idx' INFO 12:47:30,183 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-671.out INFO 12:47:34,190 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0258.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0258.rccache.bin.idx' INFO 12:47:34,190 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-673.out INFO 12:47:38,238 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0259.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0259.rccache.bin.idx' INFO 12:47:38,238 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-675.out INFO 12:47:42,147 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0260.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0260.rccache.bin.idx' INFO 12:47:42,147 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-677.out INFO 12:47:46,094 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0261.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0261.rccache.bin.idx' INFO 12:47:46,094 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-679.out INFO 12:47:50,141 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0262.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0262.rccache.bin.idx' INFO 12:47:50,141 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-681.out INFO 12:47:54,257 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0263.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0263.rccache.bin.idx' INFO 12:47:54,257 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-683.out INFO 12:47:58,403 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0264.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0264.rccache.bin.idx' INFO 12:47:58,403 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-685.out INFO 12:48:05,039 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0265.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0265.rccache.bin.idx' INFO 12:48:05,039 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-687.out INFO 12:48:08,950 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0266.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0266.rccache.bin.idx' INFO 12:48:08,951 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-689.out INFO 12:48:13,055 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0267.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0267.rccache.bin.idx' INFO 12:48:13,055 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-691.out INFO 12:48:17,166 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0268.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0268.rccache.bin.idx' INFO 12:48:17,166 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-693.out INFO 12:48:21,098 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0269.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0269.rccache.bin.idx' INFO 12:48:21,098 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-695.out INFO 12:48:24,983 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0270.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0270.rccache.bin.idx' INFO 12:48:24,983 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-697.out INFO 12:48:29,189 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0271.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0271.rccache.bin.idx' INFO 12:48:29,189 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-699.out INFO 12:48:33,157 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0272.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0272.rccache.bin.idx' INFO 12:48:33,157 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-701.out INFO 12:48:37,156 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0273.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0273.rccache.bin.idx' INFO 12:48:37,156 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-703.out INFO 12:48:41,185 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0274.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0274.rccache.bin.idx' INFO 12:48:41,185 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-705.out INFO 12:48:45,612 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0275.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0275.rccache.bin.idx' INFO 12:48:45,612 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-707.out INFO 12:48:49,882 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0276.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0276.rccache.bin.idx' INFO 12:48:49,882 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-709.out INFO 12:48:53,833 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0277.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0277.rccache.bin.idx' INFO 12:48:53,833 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-711.out INFO 12:48:57,839 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0278.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0278.rccache.bin.idx' INFO 12:48:57,839 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-713.out INFO 12:49:01,993 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0279.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0279.rccache.bin.idx' INFO 12:49:01,993 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-715.out INFO 12:49:06,076 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0280.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0280.rccache.bin.idx' INFO 12:49:06,076 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-717.out INFO 12:49:10,143 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0281.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0281.rccache.bin.idx' INFO 12:49:10,143 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-719.out INFO 12:49:14,280 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0282.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0282.rccache.bin.idx' INFO 12:49:14,280 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-721.out INFO 12:49:18,259 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0283.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0283.rccache.bin.idx' INFO 12:49:18,259 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-723.out INFO 12:49:22,429 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0284.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0284.rccache.bin.idx' INFO 12:49:22,429 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-725.out INFO 12:49:26,469 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0285.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0285.rccache.bin.idx' INFO 12:49:26,469 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-727.out INFO 12:49:30,700 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0286.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0286.rccache.bin.idx' INFO 12:49:30,700 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-729.out INFO 12:49:34,638 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0287.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0287.rccache.bin.idx' INFO 12:49:34,638 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-731.out INFO 12:49:38,776 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0288.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0288.rccache.bin.idx' INFO 12:49:38,776 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-733.out INFO 12:49:42,945 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0289.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0289.rccache.bin.idx' INFO 12:49:42,945 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-735.out INFO 12:49:46,933 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0290.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0290.rccache.bin.idx' INFO 12:49:46,933 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-737.out INFO 12:49:51,192 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0291.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0291.rccache.bin.idx' INFO 12:49:51,192 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-739.out INFO 12:49:55,235 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0292.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0292.rccache.bin.idx' INFO 12:49:55,235 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-741.out INFO 12:50:01,496 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0293.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0293.rccache.bin.idx' INFO 12:50:01,496 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-743.out INFO 12:50:05,556 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0294.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0294.rccache.bin.idx' INFO 12:50:05,556 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-745.out INFO 12:50:09,565 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0295.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0295.rccache.bin.idx' INFO 12:50:09,565 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-747.out INFO 12:50:13,540 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0296.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0296.rccache.bin.idx' INFO 12:50:13,540 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-749.out INFO 12:50:17,538 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0297.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0297.rccache.bin.idx' INFO 12:50:17,538 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-751.out INFO 12:50:21,579 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0298.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0298.rccache.bin.idx' INFO 12:50:21,579 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-753.out INFO 12:50:25,692 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0299.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0299.rccache.bin.idx' INFO 12:50:25,692 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-755.out INFO 12:50:29,732 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0300.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0300.rccache.bin.idx' INFO 12:50:29,732 FunctionEdge - Output written to /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-757.out INFO 12:50:33,597 QGraph - 178 Pend, 299 Run, 4 Fail, 452 Done INFO 12:50:33,599 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0070.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0070.rccache.bin.idx' INFO 12:50:33,599 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0158.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0158.rccache.bin.idx' INFO 12:50:33,599 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0040.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0040.rccache.bin.idx' INFO 12:50:33,599 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0180.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0180.rccache.bin.idx' INFO 12:50:33,599 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0239.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0239.rccache.bin.idx' INFO 12:50:33,600 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0015.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0015.rccache.bin.idx' INFO 12:50:33,600 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0195.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0195.rccache.bin.idx' INFO 12:50:33,600 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0107.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0107.rccache.bin.idx' INFO 12:50:33,600 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0084.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0084.rccache.bin.idx' INFO 12:50:33,601 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0092.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0092.rccache.bin.idx' INFO 12:50:33,601 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0151.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0151.rccache.bin.idx' INFO 12:50:33,601 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0098.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0098.rccache.bin.idx' INFO 12:50:33,601 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0137.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0137.rccache.bin.idx' INFO 12:50:33,601 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0288.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0288.rccache.bin.idx' INFO 12:50:33,602 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0049.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0049.rccache.bin.idx' INFO 12:50:33,602 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0114.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0114.rccache.bin.idx' INFO 12:50:33,602 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0136.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0136.rccache.bin.idx' INFO 12:50:33,602 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0010.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0010.rccache.bin.idx' INFO 12:50:33,602 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0285.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0285.rccache.bin.idx' INFO 12:50:33,603 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0234.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0234.rccache.bin.idx' INFO 12:50:33,603 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0048.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0048.rccache.bin.idx' INFO 12:50:33,603 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0211.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0211.rccache.bin.idx' INFO 12:50:33,603 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0024.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0024.rccache.bin.idx' INFO 12:50:33,603 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0068.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0068.rccache.bin.idx' INFO 12:50:33,603 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0292.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0292.rccache.bin.idx' INFO 12:50:33,604 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0255.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0255.rccache.bin.idx' INFO 12:50:33,604 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0241.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0241.rccache.bin.idx' INFO 12:50:33,604 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0102.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0102.rccache.bin.idx' INFO 12:50:33,604 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0123.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0123.rccache.bin.idx' INFO 12:50:33,604 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0167.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0167.rccache.bin.idx' INFO 12:50:33,605 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0204.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0204.rccache.bin.idx' INFO 12:50:33,605 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0202.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0202.rccache.bin.idx' INFO 12:50:33,605 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0181.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0181.rccache.bin.idx' INFO 12:50:33,605 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0190.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0190.rccache.bin.idx' INFO 12:50:33,605 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0263.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0263.rccache.bin.idx' INFO 12:50:33,605 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0146.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0146.rccache.bin.idx' INFO 12:50:33,606 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0219.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0219.rccache.bin.idx' INFO 12:50:33,606 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0111.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0111.rccache.bin.idx' INFO 12:50:33,606 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0170.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0170.rccache.bin.idx' INFO 12:50:33,606 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0220.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0220.rccache.bin.idx' INFO 12:50:33,606 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0266.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0266.rccache.bin.idx' INFO 12:50:33,607 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0275.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0275.rccache.bin.idx' INFO 12:50:33,607 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0055.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0055.rccache.bin.idx' INFO 12:50:33,607 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0066.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0066.rccache.bin.idx' INFO 12:50:33,607 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0247.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0247.rccache.bin.idx' INFO 12:50:33,607 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0253.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0253.rccache.bin.idx' INFO 12:50:33,607 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0033.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0033.rccache.bin.idx' INFO 12:50:33,608 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0187.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0187.rccache.bin.idx' INFO 12:50:33,608 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0088.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0088.rccache.bin.idx' INFO 12:50:33,608 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0154.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0154.rccache.bin.idx' INFO 12:50:33,608 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0198.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0198.rccache.bin.idx' INFO 12:50:33,608 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0165.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0165.rccache.bin.idx' INFO 12:50:33,609 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0143.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0143.rccache.bin.idx' INFO 12:50:33,609 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0155.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0155.rccache.bin.idx' INFO 12:50:33,609 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0082.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0082.rccache.bin.idx' INFO 12:50:33,609 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0121.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0121.rccache.bin.idx' INFO 12:50:33,609 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0257.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0257.rccache.bin.idx' INFO 12:50:33,609 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0243.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0243.rccache.bin.idx' INFO 12:50:33,610 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0171.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0171.rccache.bin.idx' INFO 12:50:33,610 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0273.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0273.rccache.bin.idx' INFO 12:50:33,610 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0286.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0286.rccache.bin.idx' INFO 12:50:33,610 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0237.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0237.rccache.bin.idx' INFO 12:50:33,610 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0164.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0164.rccache.bin.idx' INFO 12:50:33,611 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0009.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0009.rccache.bin.idx' INFO 12:50:33,611 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0120.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0120.rccache.bin.idx' INFO 12:50:33,611 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0039.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0039.rccache.bin.idx' INFO 12:50:33,611 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0016.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0016.rccache.bin.idx' INFO 12:50:33,611 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0127.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0127.rccache.bin.idx' INFO 12:50:33,611 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0149.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0149.rccache.bin.idx' INFO 12:50:33,612 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0072.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0072.rccache.bin.idx' INFO 12:50:33,612 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0086.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0086.rccache.bin.idx' INFO 12:50:33,612 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0130.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0130.rccache.bin.idx' INFO 12:50:33,612 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0174.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0174.rccache.bin.idx' INFO 12:50:33,612 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0259.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0259.rccache.bin.idx' INFO 12:50:33,613 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0218.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0218.rccache.bin.idx' INFO 12:50:33,613 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0023.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0023.rccache.bin.idx' INFO 12:50:33,613 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0217.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0217.rccache.bin.idx' INFO 12:50:33,613 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0135.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0135.rccache.bin.idx' INFO 12:50:33,613 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0062.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0062.rccache.bin.idx' INFO 12:50:33,613 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0284.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0284.rccache.bin.idx' INFO 12:50:33,614 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0113.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0113.rccache.bin.idx' INFO 12:50:33,614 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0129.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0129.rccache.bin.idx' INFO 12:50:33,614 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0139.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0139.rccache.bin.idx' INFO 12:50:33,614 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0117.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0117.rccache.bin.idx' INFO 12:50:33,614 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0159.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0159.rccache.bin.idx' INFO 12:50:33,615 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0161.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0161.rccache.bin.idx' INFO 12:50:33,615 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0138.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0138.rccache.bin.idx' INFO 12:50:33,615 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0293.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0293.rccache.bin.idx' INFO 12:50:33,615 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0227.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0227.rccache.bin.idx' INFO 12:50:33,615 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0183.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0183.rccache.bin.idx' INFO 12:50:33,615 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0003.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0003.rccache.bin.idx' INFO 12:50:33,616 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0205.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0205.rccache.bin.idx' INFO 12:50:33,616 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0071.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0071.rccache.bin.idx' INFO 12:50:33,616 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0271.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0271.rccache.bin.idx' INFO 12:50:33,616 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0249.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0249.rccache.bin.idx' INFO 12:50:33,616 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0013.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0013.rccache.bin.idx' INFO 12:50:33,617 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0046.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0046.rccache.bin.idx' INFO 12:50:33,617 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0178.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0178.rccache.bin.idx' INFO 12:50:33,617 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0012.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0012.rccache.bin.idx' INFO 12:50:33,617 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0233.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0233.rccache.bin.idx' INFO 12:50:33,617 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0115.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0115.rccache.bin.idx' INFO 12:50:33,618 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0027.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0027.rccache.bin.idx' INFO 12:50:33,618 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0192.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0192.rccache.bin.idx' INFO 12:50:33,618 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0145.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0145.rccache.bin.idx' INFO 12:50:33,618 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0122.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0122.rccache.bin.idx' INFO 12:50:33,618 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0056.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0056.rccache.bin.idx' INFO 12:50:33,618 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0034.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0034.rccache.bin.idx' INFO 12:50:33,619 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0080.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0080.rccache.bin.idx' INFO 12:50:33,619 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0100.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0100.rccache.bin.idx' INFO 12:50:33,619 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0078.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0078.rccache.bin.idx' INFO 12:50:33,619 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0168.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0168.rccache.bin.idx' INFO 12:50:33,619 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0184.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0184.rccache.bin.idx' INFO 12:50:33,620 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0162.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0162.rccache.bin.idx' INFO 12:50:33,620 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0225.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0225.rccache.bin.idx' INFO 12:50:33,620 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0258.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0258.rccache.bin.idx' INFO 12:50:33,620 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0250.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0250.rccache.bin.idx' INFO 12:50:33,620 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0043.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0043.rccache.bin.idx' INFO 12:50:33,620 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0052.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0052.rccache.bin.idx' INFO 12:50:33,621 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0021.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0021.rccache.bin.idx' INFO 12:50:33,621 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0177.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0177.rccache.bin.idx' INFO 12:50:33,621 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0294.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0294.rccache.bin.idx' INFO 12:50:33,622 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0087.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0087.rccache.bin.idx' INFO 12:50:33,622 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0235.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0235.rccache.bin.idx' INFO 12:50:33,622 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0030.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0030.rccache.bin.idx' INFO 12:50:33,622 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0221.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0221.rccache.bin.idx' INFO 12:50:33,622 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0265.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0265.rccache.bin.idx' INFO 12:50:33,622 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0065.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0065.rccache.bin.idx' INFO 12:50:33,623 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0019.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0019.rccache.bin.idx' INFO 12:50:33,623 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0036.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0036.rccache.bin.idx' INFO 12:50:33,623 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0267.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0267.rccache.bin.idx' INFO 12:50:33,623 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0142.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0142.rccache.bin.idx' INFO 12:50:33,623 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0278.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0278.rccache.bin.idx' INFO 12:50:33,623 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0133.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0133.rccache.bin.idx' INFO 12:50:33,624 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0251.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0251.rccache.bin.idx' INFO 12:50:33,624 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0300.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0300.rccache.bin.idx' INFO 12:50:33,624 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0094.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0094.rccache.bin.idx' INFO 12:50:33,625 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0064.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0064.rccache.bin.idx' INFO 12:50:33,625 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0096.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0096.rccache.bin.idx' INFO 12:50:33,625 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0223.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0223.rccache.bin.idx' INFO 12:50:33,625 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0006.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0006.rccache.bin.idx' INFO 12:50:33,625 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0119.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0119.rccache.bin.idx' INFO 12:50:33,625 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0274.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0274.rccache.bin.idx' INFO 12:50:33,626 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0152.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0152.rccache.bin.idx' INFO 12:50:33,626 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0201.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0201.rccache.bin.idx' INFO 12:50:33,626 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0050.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0050.rccache.bin.idx' INFO 12:50:33,626 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0207.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0207.rccache.bin.idx' INFO 12:50:33,626 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0103.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0103.rccache.bin.idx' INFO 12:50:33,627 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0059.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0059.rccache.bin.idx' INFO 12:50:33,627 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0081.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0081.rccache.bin.idx' INFO 12:50:33,627 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0191.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0191.rccache.bin.idx' INFO 12:50:33,627 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0169.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0169.rccache.bin.idx' INFO 12:50:33,627 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0026.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0026.rccache.bin.idx' INFO 12:50:33,627 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0004.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0004.rccache.bin.idx' INFO 12:50:33,628 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0042.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0042.rccache.bin.idx' INFO 12:50:33,628 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0125.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0125.rccache.bin.idx' INFO 12:50:33,628 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0147.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0147.rccache.bin.idx' INFO 12:50:33,628 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0037.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0037.rccache.bin.idx' INFO 12:50:33,628 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0054.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0054.rccache.bin.idx' INFO 12:50:33,629 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0246.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0246.rccache.bin.idx' INFO 12:50:33,629 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0224.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0224.rccache.bin.idx' INFO 12:50:33,629 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0268.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0268.rccache.bin.idx' INFO 12:50:33,629 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0093.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0093.rccache.bin.idx' INFO 12:50:33,629 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0244.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0244.rccache.bin.idx' INFO 12:50:33,630 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0005.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0005.rccache.bin.idx' INFO 12:50:33,630 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0160.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0160.rccache.bin.idx' INFO 12:50:33,630 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0200.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0200.rccache.bin.idx' INFO 12:50:33,630 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0058.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0058.rccache.bin.idx' INFO 12:50:33,630 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0020.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0020.rccache.bin.idx' INFO 12:50:33,630 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0109.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0109.rccache.bin.idx' INFO 12:50:33,631 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0197.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0197.rccache.bin.idx' INFO 12:50:33,631 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0035.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0035.rccache.bin.idx' INFO 12:50:33,631 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0175.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0175.rccache.bin.idx' INFO 12:50:33,632 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0153.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0153.rccache.bin.idx' INFO 12:50:33,632 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0079.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0079.rccache.bin.idx' INFO 12:50:33,632 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0131.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0131.rccache.bin.idx' INFO 12:50:33,632 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0213.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0213.rccache.bin.idx' INFO 12:50:33,632 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0248.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0248.rccache.bin.idx' INFO 12:50:33,632 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0290.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0290.rccache.bin.idx' INFO 12:50:33,633 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0287.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0287.rccache.bin.idx' INFO 12:50:33,633 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0156.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0156.rccache.bin.idx' INFO 12:50:33,633 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0112.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0112.rccache.bin.idx' INFO 12:50:33,633 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0022.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0022.rccache.bin.idx' INFO 12:50:33,633 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0099.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0099.rccache.bin.idx' INFO 12:50:33,634 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0281.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0281.rccache.bin.idx' INFO 12:50:33,634 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0242.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0242.rccache.bin.idx' INFO 12:50:33,634 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0095.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0095.rccache.bin.idx' INFO 12:50:33,634 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0297.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0297.rccache.bin.idx' INFO 12:50:33,634 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0073.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0073.rccache.bin.idx' INFO 12:50:33,634 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0277.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0277.rccache.bin.idx' INFO 12:50:33,635 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0051.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0051.rccache.bin.idx' INFO 12:50:33,635 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0176.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0176.rccache.bin.idx' INFO 12:50:33,635 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0209.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0209.rccache.bin.idx' INFO 12:50:33,636 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0011.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0011.rccache.bin.idx' INFO 12:50:33,636 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0029.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0029.rccache.bin.idx' INFO 12:50:33,636 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0231.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0231.rccache.bin.idx' INFO 12:50:33,636 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0077.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0077.rccache.bin.idx' INFO 12:50:33,636 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0007.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0007.rccache.bin.idx' INFO 12:50:33,636 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0044.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0044.rccache.bin.idx' INFO 12:50:33,637 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0264.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0264.rccache.bin.idx' INFO 12:50:33,637 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0236.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0236.rccache.bin.idx' INFO 12:50:33,637 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0280.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0280.rccache.bin.idx' INFO 12:50:33,637 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0014.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0014.rccache.bin.idx' INFO 12:50:33,637 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0199.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0199.rccache.bin.idx' INFO 12:50:33,638 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0148.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0148.rccache.bin.idx' INFO 12:50:33,638 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0060.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0060.rccache.bin.idx' INFO 12:50:33,638 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0038.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0038.rccache.bin.idx' INFO 12:50:33,638 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0126.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0126.rccache.bin.idx' INFO 12:50:33,638 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0132.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0132.rccache.bin.idx' INFO 12:50:33,638 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0110.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0110.rccache.bin.idx' INFO 12:50:33,639 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0193.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0193.rccache.bin.idx' INFO 12:50:33,639 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0028.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0028.rccache.bin.idx' INFO 12:50:33,639 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0262.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0262.rccache.bin.idx' INFO 12:50:33,639 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0106.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0106.rccache.bin.idx' INFO 12:50:33,639 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0053.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0053.rccache.bin.idx' INFO 12:50:33,639 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0083.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0083.rccache.bin.idx' INFO 12:50:33,640 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0097.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0097.rccache.bin.idx' INFO 12:50:33,640 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0185.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0185.rccache.bin.idx' INFO 12:50:33,640 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0296.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0296.rccache.bin.idx' INFO 12:50:33,640 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0208.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0208.rccache.bin.idx' INFO 12:50:33,640 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0067.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0067.rccache.bin.idx' INFO 12:50:33,641 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0141.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0141.rccache.bin.idx' INFO 12:50:33,641 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0229.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0229.rccache.bin.idx' INFO 12:50:33,641 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0252.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0252.rccache.bin.idx' INFO 12:50:33,641 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0116.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0116.rccache.bin.idx' INFO 12:50:33,641 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0215.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0215.rccache.bin.idx' INFO 12:50:33,642 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0261.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0261.rccache.bin.idx' INFO 12:50:33,642 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0173.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0173.rccache.bin.idx' INFO 12:50:33,642 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0018.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0018.rccache.bin.idx' INFO 12:50:33,642 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0076.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0076.rccache.bin.idx' INFO 12:50:33,643 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0172.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0172.rccache.bin.idx' INFO 12:50:33,643 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0210.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0210.rccache.bin.idx' INFO 12:50:33,643 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0276.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0276.rccache.bin.idx' INFO 12:50:33,643 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0216.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0216.rccache.bin.idx' INFO 12:50:33,643 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0025.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0025.rccache.bin.idx' INFO 12:50:33,643 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0194.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0194.rccache.bin.idx' INFO 12:50:33,644 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0260.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0260.rccache.bin.idx' INFO 12:50:33,644 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0047.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0047.rccache.bin.idx' INFO 12:50:33,644 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0238.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0238.rccache.bin.idx' INFO 12:50:33,644 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0128.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0128.rccache.bin.idx' INFO 12:50:33,644 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0254.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0254.rccache.bin.idx' INFO 12:50:33,645 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0032.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0032.rccache.bin.idx' INFO 12:50:33,645 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0188.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0188.rccache.bin.idx' INFO 12:50:33,645 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0232.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0232.rccache.bin.idx' INFO 12:50:33,645 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0150.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0150.rccache.bin.idx' INFO 12:50:33,646 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0144.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0144.rccache.bin.idx' INFO 12:50:33,646 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0166.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0166.rccache.bin.idx' INFO 12:50:33,646 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0222.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0222.rccache.bin.idx' INFO 12:50:33,646 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0291.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0291.rccache.bin.idx' INFO 12:50:33,646 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0182.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0182.rccache.bin.idx' INFO 12:50:33,647 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0226.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0226.rccache.bin.idx' INFO 12:50:33,647 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0002.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0002.rccache.bin.idx' INFO 12:50:33,647 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0189.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0189.rccache.bin.idx' INFO 12:50:33,647 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0057.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0057.rccache.bin.idx' INFO 12:50:33,647 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0101.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0101.rccache.bin.idx' INFO 12:50:33,648 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0270.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0270.rccache.bin.idx' INFO 12:50:33,648 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0282.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0282.rccache.bin.idx' INFO 12:50:33,648 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0090.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0090.rccache.bin.idx' INFO 12:50:33,648 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0134.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0134.rccache.bin.idx' INFO 12:50:33,648 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0299.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0299.rccache.bin.idx' INFO 12:50:33,648 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0203.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0203.rccache.bin.idx' INFO 12:50:33,649 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0085.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0085.rccache.bin.idx' INFO 12:50:33,649 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0212.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0212.rccache.bin.idx' INFO 12:50:33,649 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0269.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0269.rccache.bin.idx' INFO 12:50:33,649 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0289.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0289.rccache.bin.idx' INFO 12:50:33,650 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0124.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0124.rccache.bin.idx' INFO 12:50:33,650 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0074.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0074.rccache.bin.idx' ERROR 12:50:33,650 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0118.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0118.rccache.bin.idx' ERROR 12:50:33,650 FunctionEdge - Contents of /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-393.out: INFO 12:38:04,300 HelpFormatter - ----------------------------------------------------------- INFO 12:38:04,302 HelpFormatter - Program Name: org.broadinstitute.sv.apps.IndexReadCountFile INFO 12:38:04,305 HelpFormatter - Program Args: -I /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0118.rccache.bin -O /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0118.rccache.bin.idx INFO 12:38:04,306 HelpFormatter - Executing as wsh@localhost on Linux 2.6.32-696.6.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_141-b15. INFO 12:38:04,307 HelpFormatter - Date/Time: 2018/02/01 12:38:04 INFO 12:38:04,307 HelpFormatter - ----------------------------------------------------------- INFO 12:38:04,307 HelpFormatter - ----------------------------------------------------------- INFO 12:38:04,603 CommandLineProgram - Program completed. ------------------------------------------------------------------------------------------ Done. There were no warn messages. ------------------------------------------------------------------------------------------ INFO 12:50:33,650 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0140.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0140.rccache.bin.idx' INFO 12:50:33,651 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0206.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0206.rccache.bin.idx' INFO 12:50:33,651 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0214.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0214.rccache.bin.idx' INFO 12:50:33,651 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0228.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0228.rccache.bin.idx' INFO 12:50:33,651 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0245.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0245.rccache.bin.idx' INFO 12:50:33,651 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0008.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0008.rccache.bin.idx' INFO 12:50:33,652 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0063.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0063.rccache.bin.idx' INFO 12:50:33,652 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0041.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0041.rccache.bin.idx' INFO 12:50:33,652 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0272.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0272.rccache.bin.idx' INFO 12:50:33,652 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0279.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0279.rccache.bin.idx' INFO 12:50:33,652 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0001.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0001.rccache.bin.idx' INFO 12:50:33,652 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0075.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0075.rccache.bin.idx' INFO 12:50:33,653 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0295.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0295.rccache.bin.idx' INFO 12:50:33,653 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0240.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0240.rccache.bin.idx' INFO 12:50:33,653 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0031.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0031.rccache.bin.idx' INFO 12:50:33,653 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0105.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0105.rccache.bin.idx' INFO 12:50:33,653 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0256.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0256.rccache.bin.idx' INFO 12:50:33,654 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0186.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0186.rccache.bin.idx' INFO 12:50:33,654 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0157.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0157.rccache.bin.idx' INFO 12:50:33,654 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0069.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0069.rccache.bin.idx' INFO 12:50:33,654 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0163.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0163.rccache.bin.idx' INFO 12:50:33,654 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0091.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0091.rccache.bin.idx' INFO 12:50:33,655 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0089.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0089.rccache.bin.idx' INFO 12:50:33,655 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0179.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0179.rccache.bin.idx' INFO 12:50:33,655 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0045.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0045.rccache.bin.idx' INFO 12:50:33,655 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0196.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0196.rccache.bin.idx' INFO 12:50:33,655 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0108.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0108.rccache.bin.idx' INFO 12:50:33,655 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0230.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0230.rccache.bin.idx' INFO 12:50:33,656 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0061.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0061.rccache.bin.idx' INFO 12:50:33,656 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0017.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0017.rccache.bin.idx' INFO 12:50:33,656 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0283.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0283.rccache.bin.idx' INFO 12:50:33,657 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0298.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0298.rccache.bin.idx' INFO 12:50:33,657 QGraph - Writing incremental jobs reports... INFO 12:50:33,665 QGraph - 178 Pend, 0 Run, 5 Fail, 750 Done INFO 12:50:33,669 QCommandLine - Writing final jobs report... INFO 12:50:33,669 QCommandLine - Done with errors INFO 12:50:33,679 QGraph - ------- INFO 12:50:33,679 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0118.rccache.bin' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0118.rccache.bin.idx' INFO 12:50:33,679 QGraph - Log: /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-393.out INFO 12:50:33,680 QGraph - ------- INFO 12:50:33,680 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadCounts' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.list' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/rccache.merge/P0104.rccache.bin' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' -L 5:170000001-180000000 INFO 12:50:33,680 QGraph - Log: /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-364.out INFO 12:50:33,680 QGraph - ------- INFO 12:50:33,681 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeGCProfiles' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120044-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120057-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120074-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120079-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/2017120090-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK2CK4-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK3-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK4-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CK5-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120087-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120089-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120092-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120093-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120098-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120106-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120108-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120111-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120114-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120115-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120120-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120121-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120122-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120123-IEMS.dedupped.bam.gcprof.zip' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofile/CX2017120132-IEMS.dedupped.bam.gcprof.zip' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/gcprofiles.zip' INFO 12:50:33,681 QGraph - Log: /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-108.out INFO 12:50:33,681 QGraph - ------- INFO 12:50:33,681 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.fasta' '-I' '/work1/wsh/4.test/1.perl/1.pipetest/IEMS/bam/2017120044-IEMS.dedupped.bam' '-O' '/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/depth/2017120044-IEMS.dedupped.depth.txt' '-disableGATKTraversal' 'true' '-md' 'IEMS/metadata' '-ploidyMapFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.ploidymap.txt' '-configFile' 'conf/genstrip_parameters.txt' '-genomeMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.svmask.fasta' '-readDepthMaskFile' '/work/wsh/0.Pipeline/TargetSeq/Genome_STRiP_ref/Homo_sapiens_assembly19.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 12:50:33,681 QGraph - Log: /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/logs/SVPreprocess-34.out INFO 12:50:33,681 QGraph - ------- INFO 12:50:33,681 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/tmpdir_SVPreprocess' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' '-cp' '/work/SoftW/svtoolkit/lib/SVToolkit.jar:/work/SoftW/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/work/SoftW/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.SVToolkitInfo' INFO 12:50:33,682 QGraph - Log: /work1/wsh/4.test/1.perl/1.pipetest/test/IEMS/metadata/svtoolkit.version.dat INFO 12:50:33,682 QCommandLine - Script failed: 178 Pend, 0 Run, 5 Fail, 750 Done ------------------------------------------------------------------------------------------ Done. There were no warn messages. ------------------------------------------------------------------------------------------