INFO 21:33:15,876 QScriptManager - Compiling 2 QScripts INFO 21:33:29,297 QScriptManager - Compilation complete INFO 21:33:29,457 HelpFormatter - ---------------------------------------------------------------------- INFO 21:33:29,458 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/02/06 10:59:46 INFO 21:33:29,459 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 21:33:29,459 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 21:33:29,461 HelpFormatter - Program Args: -S /home/ligw/tools/svtoolkit2.1553/svtoolkit/qscript/SVPreprocess.q -S /home/ligw/tools/svtoolkit2.1553/svtoolkit/qscript/SVQScript.q -gatk /home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar --disableJobReport -cp /home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir.chr04.rice -R data/rice7_reference.fasta -genomeMaskFile data/rice7_reference_svmask.fasta -readDepthMaskFile data/rice7_reference_rdmask.bed -genderMapFile data/input_bam_files_gender.map -runDirectory rice_chr04_discovery -md rice_chr04_discovery/metadata -disableGATKTraversal -useMultiStep -L chr04 -reduceInsertSizeDistributions true -computeReadCounts true -computeGCProfiles true -jobLogDir rice_chr04_discovery/logs -I data/input_bam_files.list -run INFO 21:33:29,472 HelpFormatter - Executing as ligw@node13 on Linux 2.6.32-504.3.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_20-b26. INFO 21:33:29,474 HelpFormatter - Date/Time: 2015/02/13 21:33:29 INFO 21:33:29,474 HelpFormatter - ---------------------------------------------------------------------- INFO 21:33:29,474 HelpFormatter - ---------------------------------------------------------------------- INFO 21:33:29,493 QCommandLine - Scripting SVPreprocess INFO 21:33:30,408 QCommandLine - Added 151 functions INFO 21:33:30,408 QGraph - Generating graph. INFO 21:33:30,503 QGraph - Running jobs. INFO 21:33:30,569 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadSpanCoverage' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW1.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW2.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW3.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW4.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW5.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW6.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW7.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW8.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW9.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW10.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW11.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW12.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW13.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW14.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW15.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW16.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW17.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW18.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW19.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW20.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW21.reheader.spans.txt' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans.dat' INFO 21:33:30,569 FunctionEdge - Output written to /home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/logs/SVPreprocess-71.out INFO 21:33:36,012 QGraph - 5 Pend, 1 Run, 0 Fail, 145 Done INFO 21:34:00,570 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadSpanCoverage' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW1.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW2.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW3.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW4.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW5.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW6.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW7.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW8.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW9.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW10.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW11.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW12.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW13.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW14.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW15.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW16.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW17.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW18.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW19.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW20.reheader.spans.txt' '-I' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans/LGW21.reheader.spans.txt' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/spans.dat' INFO 21:34:00,573 QGraph - Writing incremental jobs reports... INFO 21:34:00,581 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeDepthProfiles' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/profiles_100Kb/profile_seq_chr04_100000.dat.gz' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW1.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW2.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW3.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW4.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW5.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW6.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW7.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW8.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW9.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW10.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW11.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW12.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW13.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW14.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW15.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW16.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW17.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW18.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW19.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW20.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW21.reheader.bam' '-configFile' 'conf/genstrip_installtest_parameters.txt' '-R' 'data/rice7_reference.fasta' '-L' 'chr04:0-0' '-genomeMaskFile' 'data/rice7_reference_svmask.fasta' '-md' 'rice_chr04_discovery/metadata' '-genderMapFile' 'data/input_bam_files_gender.map' '-profileBinSize' '100000' '-maximumReferenceGapLength' '10000' INFO 21:34:00,581 FunctionEdge - Output written to /home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/logs/SVPreprocess-147.out INFO 21:36:50,259 QGraph - 4 Pend, 1 Run, 0 Fail, 146 Done INFO 21:36:50,263 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeDepthProfiles' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/profiles_100Kb/profile_seq_chr04_100000.dat.gz' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW1.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW2.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW3.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW4.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW5.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW6.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW7.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW8.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW9.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW10.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW11.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW12.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW13.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW14.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW15.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW16.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW17.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW18.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW19.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW20.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW21.reheader.bam' '-configFile' 'conf/genstrip_installtest_parameters.txt' '-R' 'data/rice7_reference.fasta' '-L' 'chr04:0-0' '-genomeMaskFile' 'data/rice7_reference_svmask.fasta' '-md' 'rice_chr04_discovery/metadata' '-genderMapFile' 'data/input_bam_files_gender.map' '-profileBinSize' '100000' '-maximumReferenceGapLength' '10000' INFO 21:36:50,263 QGraph - Writing incremental jobs reports... INFO 21:36:50,270 FunctionEdge - Starting: tabix -f -S 1 -s 2 -b 3 -e 4 rice_chr04_discovery/metadata/profiles_100Kb/profile_seq_chr04_100000.dat.gz INFO 21:36:50,271 FunctionEdge - Output written to /home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/logs/SVPreprocess-148.out INFO 21:36:50,301 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CallSampleGender' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/sample_gender.report.dat' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW1.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW2.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW3.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW4.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW5.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW6.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW7.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW8.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW9.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW10.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW11.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW12.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW13.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW14.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW15.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW16.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW17.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW18.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW19.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW20.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW21.reheader.bam' '-R' 'data/rice7_reference.fasta' '-md' 'rice_chr04_discovery/metadata' '-genomeMaskFile' 'data/rice7_reference_svmask.fasta' '-genomeInterval' 'chr04' '-ploidyMapFile' 'data/rice7_reference.ploidymap.txt' '-minMapQ' '10' INFO 21:36:50,302 FunctionEdge - Output written to /home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/logs/SVPreprocess-150.out INFO 21:36:56,492 QGraph - 2 Pend, 2 Run, 0 Fail, 147 Done INFO 21:37:20,264 FunctionEdge - Done: tabix -f -S 1 -s 2 -b 3 -e 4 rice_chr04_discovery/metadata/profiles_100Kb/profile_seq_chr04_100000.dat.gz INFO 21:37:20,267 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CallSampleGender' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/sample_gender.report.dat' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW1.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW2.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW3.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW4.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW5.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW6.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW7.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW8.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW9.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW10.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW11.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW12.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW13.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW14.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW15.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW16.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW17.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW18.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW19.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW20.reheader.bam' '-I' '/home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW21.reheader.bam' '-R' 'data/rice7_reference.fasta' '-md' 'rice_chr04_discovery/metadata' '-genomeMaskFile' 'data/rice7_reference_svmask.fasta' '-genomeInterval' 'chr04' '-ploidyMapFile' 'data/rice7_reference.ploidymap.txt' '-minMapQ' '10' INFO 21:37:20,267 QGraph - Writing incremental jobs reports... INFO 21:37:20,274 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeSampleReadDepth' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/profiles_100Kb/rd.dat' '-profileDirectory' 'rice_chr04_discovery/metadata/profiles_100Kb' '-profileBinSize' '100000' '-sequence' 'chr04' INFO 21:37:20,274 FunctionEdge - Output written to /home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/logs/SVPreprocess-149.out INFO 21:37:26,325 FunctionEdge - Starting: 'Rscript' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/R/metadata/plot_chr_vs_chr_readdepth.R' 'rice_chr04_discovery/metadata/sample_gender.report.dat' 'rice_chr04_discovery/metadata/chrY_vs_chrX.pdf' 'seq_Y vs. seq_X Read Depth' 'DOSAGE_X' 'DOSAGE_Y' INFO 21:37:26,325 FunctionEdge - Output written to /home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/logs/SVPreprocess-151.out INFO 21:37:26,501 QGraph - 0 Pend, 2 Run, 0 Fail, 149 Done INFO 21:37:50,265 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeSampleReadDepth' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/metadata/profiles_100Kb/rd.dat' '-profileDirectory' 'rice_chr04_discovery/metadata/profiles_100Kb' '-profileBinSize' '100000' '-sequence' 'chr04' INFO 21:37:50,267 FunctionEdge - Done: 'Rscript' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/R/metadata/plot_chr_vs_chr_readdepth.R' 'rice_chr04_discovery/metadata/sample_gender.report.dat' 'rice_chr04_discovery/metadata/chrY_vs_chrX.pdf' 'seq_Y vs. seq_X Read Depth' 'DOSAGE_X' 'DOSAGE_Y' INFO 21:37:50,267 QGraph - Writing incremental jobs reports... INFO 21:37:50,271 QGraph - 0 Pend, 0 Run, 0 Fail, 151 Done INFO 21:37:50,276 QCommandLine - Writing final jobs report... INFO 21:37:50,279 QCommandLine - Script completed successfully with 151 total jobs INFO 21:37:58,860 QScriptManager - Compiling 2 QScripts INFO 21:38:09,870 QScriptManager - Compilation complete INFO 21:38:10,027 HelpFormatter - ---------------------------------------------------------------------- INFO 21:38:10,028 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/02/06 10:59:46 INFO 21:38:10,028 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 21:38:10,029 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 21:38:10,030 HelpFormatter - Program Args: -S /home/ligw/tools/svtoolkit2.1553/svtoolkit/qscript/SVDiscovery.q -S /home/ligw/tools/svtoolkit2.1553/svtoolkit/qscript/SVQScript.q -gatk /home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar --disableJobReport -cp /home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir.chr04.rice -R data/rice7_reference.fasta -genomeMaskFile data/rice7_reference_svmask.fasta -genderMapFile data/input_bam_files_gender.map -runDirectory rice_chr04_discovery -P select.validateReadPairs:false -md rice_chr04_discovery/metadata -disableGATKTraversal -L chr04 -jobLogDir rice_chr04_discovery/logs -minimumSize 100 -maximumSize 1000000 -suppressVCFCommandLines -I data/input_bam_files.list -O rice.chr04.discovery.vcf -run INFO 21:38:10,033 HelpFormatter - Executing as ligw@node13 on Linux 2.6.32-504.3.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_20-b26. INFO 21:38:10,033 HelpFormatter - Date/Time: 2015/02/13 21:38:10 INFO 21:38:10,034 HelpFormatter - ---------------------------------------------------------------------- INFO 21:38:10,034 HelpFormatter - ---------------------------------------------------------------------- INFO 21:38:10,049 QCommandLine - Scripting SVDiscovery INFO 21:38:10,262 QCommandLine - Added 2 functions INFO 21:38:10,262 QGraph - Generating graph. INFO 21:38:10,286 QGraph - Running jobs. INFO 21:38:10,334 FunctionEdge - Starting: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/data/rice7_reference.fasta' '-I' 'data/input_bam_files.list' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/rice.chr04.discovery.unfiltered.vcf' '-disableGATKTraversal' 'true' '-md' 'rice_chr04_discovery/metadata' '-configFile' 'conf/genstrip_installtest_parameters.txt' '-P' 'select.validateReadPairs:false' '-runDirectory' 'rice_chr04_discovery' '-genderMapFile' 'data/input_bam_files_gender.map' '-genomeMaskFile' 'data/rice7_reference_svmask.fasta' '-L' 'chr04' '-runFilePrefix' 'rice.chr04' '-searchLocus' 'chr04' '-searchWindow' 'chr04' '-searchMinimumSize' '100' '-searchMaximumSize' '1000000' INFO 21:38:10,335 FunctionEdge - Output written to /home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/logs/SVDiscovery-1.out INFO 22:14:06,735 QGraph - 1 Pend, 1 Run, 0 Fail, 0 Done INFO 22:14:06,745 FunctionEdge - Done: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/data/rice7_reference.fasta' '-I' 'data/input_bam_files.list' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/rice.chr04.discovery.unfiltered.vcf' '-disableGATKTraversal' 'true' '-md' 'rice_chr04_discovery/metadata' '-configFile' 'conf/genstrip_installtest_parameters.txt' '-P' 'select.validateReadPairs:false' '-runDirectory' 'rice_chr04_discovery' '-genderMapFile' 'data/input_bam_files_gender.map' '-genomeMaskFile' 'data/rice7_reference_svmask.fasta' '-L' 'chr04' '-runFilePrefix' 'rice.chr04' '-searchLocus' 'chr04' '-searchWindow' 'chr04' '-searchMinimumSize' '100' '-searchMaximumSize' '1000000' INFO 22:14:06,751 QGraph - Writing incremental jobs reports... INFO 22:14:06,754 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-jar' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar' '-T' 'VariantFiltration' -no_cmdline_in_header '-V' 'rice_chr04_discovery/rice.chr04.discovery.unfiltered.vcf' '-o' 'rice.chr04.discovery.vcf' '-R' 'data/rice7_reference.fasta' -filterName COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || GSDEPTHCALLTHRESHOLD >= 1.0" -filterName COHERENCE -filter "GSCOHPVALUE == \"NA\" || GSCOHPVALUE <= 0.01" -filterName DEPTHPVAL -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE >= 0.01" -filterName DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO > 0.8 || (GSDEPTHRATIO > 0.63 && (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE >= 0.01))" -filterName PAIRSPERSAMPLE -filter "GSNPAIRS <= 1.1 * GSNSAMPLES" INFO 22:14:06,754 FunctionEdge - Output written to /home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/logs/SVDiscovery-2.out INFO 22:15:10,200 QGraph - 0 Pend, 1 Run, 0 Fail, 1 Done INFO 22:15:10,204 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-jar' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar' '-T' 'VariantFiltration' -no_cmdline_in_header '-V' 'rice_chr04_discovery/rice.chr04.discovery.unfiltered.vcf' '-o' 'rice.chr04.discovery.vcf' '-R' 'data/rice7_reference.fasta' -filterName COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || GSDEPTHCALLTHRESHOLD >= 1.0" -filterName COHERENCE -filter "GSCOHPVALUE == \"NA\" || GSCOHPVALUE <= 0.01" -filterName DEPTHPVAL -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE >= 0.01" -filterName DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO > 0.8 || (GSDEPTHRATIO > 0.63 && (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE >= 0.01))" -filterName PAIRSPERSAMPLE -filter "GSNPAIRS <= 1.1 * GSNSAMPLES" INFO 22:15:10,205 QGraph - Writing incremental jobs reports... INFO 22:15:10,206 QGraph - 0 Pend, 0 Run, 0 Fail, 2 Done INFO 22:15:10,208 QCommandLine - Writing final jobs report... INFO 22:15:10,214 QCommandLine - Script completed successfully with 2 total jobs INFO 22:15:18,395 QScriptManager - Compiling 2 QScripts INFO 22:15:28,769 QScriptManager - Compilation complete INFO 22:15:28,915 HelpFormatter - ---------------------------------------------------------------------- INFO 22:15:28,916 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/02/06 10:59:46 INFO 22:15:28,916 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 22:15:28,916 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 22:15:28,917 HelpFormatter - Program Args: -S /home/ligw/tools/svtoolkit2.1553/svtoolkit/qscript/SVGenotyper.q -S /home/ligw/tools/svtoolkit2.1553/svtoolkit/qscript/SVQScript.q -gatk /home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar --disableJobReport -cp /home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir.chr04.rice -R data/rice7_reference.fasta -genomeMaskFile data/rice7_reference_svmask.fasta -genderMapFile data/input_bam_files_gender.map -runDirectory rice_chr04_discovery -md rice_chr04_discovery/metadata -disableGATKTraversal -jobLogDir rice_chr04_discovery/logs -I data/input_bam_files.list -vcf rice.chr04.discovery.vcf -O rice.chr04.genotypes.vcf -run INFO 22:15:28,920 HelpFormatter - Executing as ligw@node13 on Linux 2.6.32-504.3.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_20-b26. INFO 22:15:28,920 HelpFormatter - Date/Time: 2015/02/13 22:15:28 INFO 22:15:28,920 HelpFormatter - ---------------------------------------------------------------------- INFO 22:15:28,921 HelpFormatter - ---------------------------------------------------------------------- INFO 22:15:28,931 QCommandLine - Scripting SVGenotyper INFO 22:15:29,044 QCommandLine - Added 1 functions INFO 22:15:29,045 QGraph - Generating graph. INFO 22:15:29,059 QGraph - Running jobs. INFO 22:15:29,100 FunctionEdge - Starting: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVGenotyper '-T' 'SVGenotyperWalker' '-R' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/data/rice7_reference.fasta' '-I' 'data/input_bam_files.list' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice.chr04.genotypes.vcf' '-disableGATKTraversal' 'true' '-md' 'rice_chr04_discovery/metadata' '-configFile' 'conf/genstrip_installtest_parameters.txt' '-runDirectory' 'rice_chr04_discovery' '-genderMapFile' 'data/input_bam_files_gender.map' '-ploidyMapFile' 'data/rice7_reference.ploidymap.txt' '-genomeMaskFile' 'data/rice7_reference_svmask.fasta' '-vcf' 'rice.chr04.discovery.vcf' INFO 22:15:29,101 FunctionEdge - Output written to /home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/logs/SVGenotyper-1.out INFO 22:16:16,457 QGraph - 0 Pend, 1 Run, 0 Fail, 0 Done ERROR 22:16:16,469 FunctionEdge - Error: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVGenotyper '-T' 'SVGenotyperWalker' '-R' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/data/rice7_reference.fasta' '-I' 'data/input_bam_files.list' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice.chr04.genotypes.vcf' '-disableGATKTraversal' 'true' '-md' 'rice_chr04_discovery/metadata' '-configFile' 'conf/genstrip_installtest_parameters.txt' '-runDirectory' 'rice_chr04_discovery' '-genderMapFile' 'data/input_bam_files_gender.map' '-ploidyMapFile' 'data/rice7_reference.ploidymap.txt' '-genomeMaskFile' 'data/rice7_reference_svmask.fasta' '-vcf' 'rice.chr04.discovery.vcf' ERROR 22:16:16,478 FunctionEdge - Contents of /home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/logs/SVGenotyper-1.out: INFO 22:15:35,400 GenomeAnalysisEngine - Preparing for traversal INFO 22:15:35,402 GenomeAnalysisEngine - Done preparing for traversal INFO 22:15:35,402 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 22:15:35,402 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 22:15:35,402 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 22:15:35,408 SVGenotyper - Opening reference sequence ... INFO 22:15:35,409 SVGenotyper - Opened reference sequence. INFO 22:15:35,409 SVGenotyper - Opening genome mask ... INFO 22:15:35,410 SVGenotyper - Opened genome mask. INFO 22:15:35,410 SVGenotyper - Initializing input data set ... INFO 22:15:35,482 SVGenotyper - Initialized data set: 21 files, 370 read groups, 21 samples. INFO 22:15:35,484 MetaData - Opening metadata ... INFO 22:15:35,484 MetaData - Adding metadata directory rice_chr04_discovery/metadata ... INFO 22:15:35,486 MetaData - Opened metadata. INFO 22:15:35,528 SVGenotyper - Using copy number confidence threshold: none INFO 22:15:35,531 MetaData - Loading insert size distributions ... #INFO: ReadCountAlgorithm: detected metadata version 1, forcing legacy behavior #INFO: ReadCountAlgorithm: detected metadata version 1, forcing legacy behavior INFO 22:15:35,612 ReadCountDiskCache - Initializing read count disk cache [rice_chr04_discovery/metadata/rccache.bin] ... INFO 22:15:35,613 ReadCountDiskCache - Initialized read count disk cache with 1 file. INFO 22:15:35,707 SVGenotyper - Enabling GC normalization: 41 profiles loaded. INFO 22:15:35,859 SVGenotyper - Genotyping site: CNP DEL_1 DEL chr04 10910 10922 656790 656802 INFO 22:15:35,861 SVGenotyper - GenotypingDeletionDepthModule processing site DEL_1 ... #DBG: Fri Feb 13 22:15:35 CST 2015 RCC start: 1 #DBG: Fri Feb 13 22:15:36 CST 2015 RCC done: 1 INFO 22:15:36,352 SVGenotyper - Computing expected counts ... INFO 22:15:38,998 SVGenotyper - Computing expected counts done. INFO 22:15:39,004 SVGenotyper - Computing effective length ... INFO 22:15:39,010 SVGenotyper - Computing mixture model for DEL_1 ... INFO 22:15:39,327 SVGenotyper - Mixture model computation done. INFO 22:15:42,852 SVGenotyper - Genotyping site: CNP DEL_2 DEL chr04 87579 87609 89064 89094 INFO 22:15:42,853 SVGenotyper - GenotypingDeletionDepthModule processing site DEL_2 ... #DBG: Fri Feb 13 22:15:42 CST 2015 RCC start: 1 #DBG: Fri Feb 13 22:15:42 CST 2015 RCC done: 1 INFO 22:15:42,863 SVGenotyper - Computing expected counts ... INFO 22:15:42,872 SVGenotyper - Computing expected counts done. INFO 22:15:42,872 SVGenotyper - Computing effective length ... INFO 22:15:42,872 SVGenotyper - Computing mixture model for DEL_2 ... INFO 22:15:43,182 SVGenotyper - Mixture model computation done. INFO 22:15:43,657 SVGenotyper - Genotyping site: CNP DEL_3 DEL chr04 133685 133687 138968 138970 INFO 22:15:43,657 SVGenotyper - GenotypingDeletionDepthModule processing site DEL_3 ... #DBG: Fri Feb 13 22:15:43 CST 2015 RCC start: 1 #DBG: Fri Feb 13 22:15:43 CST 2015 RCC done: 1 INFO 22:15:43,666 SVGenotyper - Computing expected counts ... INFO 22:15:43,687 SVGenotyper - Computing expected counts done. INFO 22:15:43,687 SVGenotyper - Computing effective length ... INFO 22:15:43,687 SVGenotyper - Computing mixture model for DEL_3 ... INFO 22:15:43,996 SVGenotyper - Mixture model computation done. INFO 22:15:44,565 SVGenotyper - Genotyping site: CNP DEL_4 DEL chr04 244166 244168 245474 245476 INFO 22:15:44,566 SVGenotyper - GenotypingDeletionDepthModule processing site DEL_4 ... #DBG: Fri Feb 13 22:15:44 CST 2015 RCC start: 1 #DBG: Fri Feb 13 22:15:44 CST 2015 RCC done: 1 INFO 22:15:44,570 SVGenotyper - Computing expected counts ... INFO 22:15:44,576 SVGenotyper - Computing expected counts done. INFO 22:15:44,576 SVGenotyper - Computing effective length ... INFO 22:15:44,576 SVGenotyper - Computing mixture model for DEL_4 ... INFO 22:15:44,875 SVGenotyper - Mixture model computation done. #DBG: HWI-ST1395:98:c27wjacxx:7:2201:17052:11013 2147 chr04 244009 45 30M70H = 244075 159 CATTCAAATGTCACTACTACACAAAATCTA @CCFFFFFHHDHHJJJJJJJJJJJJIJJJJ SA:Z:chr04,244074,+,43S57M,45,4; MD:Z:30 RG:Z:840071LGW6_GGCTAC_L007_017 NM:i:0 AS:i:30 XS:i:0 #DBG: HWI-ST1395:98:c27wjacxx:7:2201:17052:11013 99 chr04 244074 45 43S57M = 244075 94 CATTCAAATGTCACTACTACACAAAATCTACAAATGTGCCGTTTTTTCCAACCGGCATCATGGAGGCGACACTGATCAAAAGGCTCATCGGTGCCGAATT @CCFFFFFHHDHHJJJJJJJJJJJJIJJJJJJJJJIGIIJIGGIIJJJIIIJJIJJJHHHHFFFFFDDDDDDDDDACDCDCDBBCBDDDDBBDDCDDBDD SA:Z:chr04,244009,+,30M70S,45,0; MD:Z:17C0A6G9G21 RG:Z:840071LGW6_GGCTAC_L007_017 NM:i:4 AS:i:37 XS:i:0 #DBG: Error processing sample: LGW6 #DBG: Error processing input file: /home/ligw/ijcross/seq_alin/bwamap/reheader_bam/LGW6.reheader.bam Error: Exception processing cnp: Right read of read pair fails right read test: HWI-ST1395:98:c27wjacxx:7:2201:17052:11013 99 chr04 244074 45 43S57M = 244075 94 CATTCAAATGTCACTACTACACAAAATCTACAAATGTGCCGTTTTTTCCAACCGGCATCATGGAGGCGACACTGATCAAAAGGCTCATCGGTGCCGAATT @CCFFFFFHHDHHJJJJJJJJJJJJIJJJJJJJJJIGIIJIGGIIJJJIIIJJIJJJHHHHFFFFFDDDDDDDDDACDCDCDBBCBDDDDBBDDCDDBDD SA:Z:chr04,244009,+,30M70S,45,0; MD:Z:17C0A6G9G21 RG:Z:840071LGW6_GGCTAC_L007_017 NM:i:4 AS:i:37 XS:i:0 CNP: DEL_4 chr04:244166-245476 INFO 22:16:05,408 ProgressMeter - Starting 0.0 30.0 s 49.6 w 100.0% 30.0 s 0.0 s ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.IllegalArgumentException: Right read of read pair fails right read test: HWI-ST1395:98:c27wjacxx:7:2201:17052:11013 99 chr04 244074 45 43S57M = 244075 94 CATTCAAATGTCACTACTACACAAAATCTACAAATGTGCCGTTTTTTCCAACCGGCATCATGGAGGCGACACTGATCAAAAGGCTCATCGGTGCCGAATT @CCFFFFFHHDHHJJJJJJJJJJJJIJJJJJJJJJIGIIJIGGIIJJJIIIJJIJJJHHHHFFFFFDDDDDDDDDACDCDCDBBCBDDDDBBDDCDDBDD SA:Z:chr04,244009,+,30M70S,45,0; MD:Z:17C0A6G9G21 RG:Z:840071LGW6_GGCTAC_L007_017 NM:i:4 AS:i:37 XS:i:0 at org.broadinstitute.sv.util.ReadPair.create(ReadPair.java:145) at org.broadinstitute.sv.genotyping.ReadPairMapper.collectReadPairs(ReadPairMapper.java:317) at org.broadinstitute.sv.genotyping.ReadPairMapper.getReadPairs(ReadPairMapper.java:181) at org.broadinstitute.sv.genotyping.ReadPairMapper.getReadPairs(ReadPairMapper.java:106) at org.broadinstitute.sv.genotyping.GenotypingReadPairModule.getReadPairs(GenotypingReadPairModule.java:200) at org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeSample(GenotypingReadPairModule.java:93) at org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeCnp(GenotypingReadPairModule.java:63) at org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeCnp(GenotypingReadPairModule.java:38) at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnpInternal(GenotypingAlgorithm.java:140) at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnp(GenotypingAlgorithm.java:105) at org.broadinstitute.sv.genotyping.SVGenotyperWalker.processVCFFile(SVGenotyperWalker.java:265) at org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:211) at org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:56) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:106) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:125) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:79) at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21) ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version ): ##### ERROR ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem. ##### ERROR If not, please post the error message, with stack trace, to the GATK forum. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: Right read of read pair fails right read test: HWI-ST1395:98:c27wjacxx:7:2201:17052:11013 99 chr04 244074 45 43S57M = 244075 94 CATTCAAATGTCACTACTACACAAAATCTACAAATGTGCCGTTTTTTCCAACCGGCATCATGGAGGCGACACTGATCAAAAGGCTCATCGGTGCCGAATT @CCFFFFFHHDHHJJJJJJJJJJJJIJJJJJJJJJIGIIJIGGIIJJJIIIJJIJJJHHHHFFFFFDDDDDDDDDACDCDCDBBCBDDDDBBDDCDDBDD SA:Z:chr04,244009,+,30M70S,45,0; MD:Z:17C0A6G9G21 RG:Z:840071LGW6_GGCTAC_L007_017 NM:i:4 AS:i:37 XS:i:0 ##### ERROR ------------------------------------------------------------------------------------------ INFO 22:16:16,481 QGraph - Writing incremental jobs reports... INFO 22:16:16,481 QGraph - 0 Pend, 0 Run, 1 Fail, 0 Done INFO 22:16:16,483 QCommandLine - Writing final jobs report... INFO 22:16:16,484 QCommandLine - Done with errors INFO 22:16:16,485 QGraph - ------- INFO 22:16:16,487 QGraph - Failed: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/tmpdir.chr04.rice' '-cp' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/SVToolkit.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/ligw/tools/svtoolkit2.1553/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVGenotyper '-T' 'SVGenotyperWalker' '-R' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/data/rice7_reference.fasta' '-I' 'data/input_bam_files.list' '-O' '/home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice.chr04.genotypes.vcf' '-disableGATKTraversal' 'true' '-md' 'rice_chr04_discovery/metadata' '-configFile' 'conf/genstrip_installtest_parameters.txt' '-runDirectory' 'rice_chr04_discovery' '-genderMapFile' 'data/input_bam_files_gender.map' '-ploidyMapFile' 'data/rice7_reference.ploidymap.txt' '-genomeMaskFile' 'data/rice7_reference_svmask.fasta' '-vcf' 'rice.chr04.discovery.vcf' INFO 22:16:16,487 QGraph - Log: /home/ligw/tools/svtoolkit2.1553/svtoolkit/workend/rice_chr04_discovery/logs/SVGenotyper-1.out INFO 22:16:16,488 QCommandLine - Script failed: 0 Pend, 0 Run, 1 Fail, 0 Done