INFO 17:48:59,280 QScriptManager - Compiling 2 QScripts INFO 17:49:12,956 QScriptManager - Compilation complete INFO 17:49:13,036 HelpFormatter - ---------------------------------------------------------------------- INFO 17:49:13,036 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/03/15 21:58:08 INFO 17:49:13,036 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 17:49:13,037 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 17:49:13,037 HelpFormatter - Program Args: -S /disk/disk1/work/xiayan/bin/svtoolkit/qscript/SVPreprocess.q -S /disk/disk1/work/xiayan/bin/svtoolkit/qscript/SVQScript.q -cp /disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar -gatk /disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -configFile /disk/disk1/work/xiayan/bin/svtoolkit/conf/genstrip_parameters.txt -tempDir /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR -R /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/population.list -md /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata -runDirectory /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1 -useMultiStep -reduceInsertSizeDistributions true -computeReadCounts true -jobLogDir /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs -computeGCProfiles true -jobRunner Shell -gatkJobRunner Shell -run INFO 17:49:13,038 HelpFormatter - Executing as xiayan@localhost.localdomain on Linux 2.6.32-431.3.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_45-mockbuild_2013_11_22_18_30-b00. INFO 17:49:13,038 HelpFormatter - Date/Time: 2015/05/08 17:49:13 INFO 17:49:13,038 HelpFormatter - ---------------------------------------------------------------------- INFO 17:49:13,038 HelpFormatter - ---------------------------------------------------------------------- INFO 17:49:13,046 QCommandLine - Scripting SVPreprocess INFO 17:49:20,251 QCommandLine - Added 6747 functions INFO 17:49:20,251 QGraph - Generating graph. INFO 17:49:20,996 QGraph - Running jobs. INFO 17:49:22,647 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/gcprofile/reference.gcprof.zip' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-writeReferenceProfile' 'true' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-copyNumberMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.gcmask.fasta' '-configFile' '/disk/disk1/work/xiayan/bin/svtoolkit/conf/genstrip_parameters.txt' INFO 17:49:22,648 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-5.out INFO 17:51:17,271 QGraph - 6742 Pend, 1 Run, 0 Fail, 4 Done ERROR 17:51:17,280 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/gcprofile/reference.gcprof.zip' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-writeReferenceProfile' 'true' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-copyNumberMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.gcmask.fasta' '-configFile' '/disk/disk1/work/xiayan/bin/svtoolkit/conf/genstrip_parameters.txt' ERROR 17:51:17,284 FunctionEdge - Contents of /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-5.out: INFO 17:49:29,319 HelpFormatter - ---------------------------------------------------------- INFO 17:49:29,322 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ComputeGCProfiles INFO 17:49:29,328 HelpFormatter - Program Args: -O /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/gcprofile/reference.gcprof.zip -R /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta -md /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata -writeReferenceProfile true -genomeMaskFile /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta -copyNumberMaskFile /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.gcmask.fasta -configFile /disk/disk1/work/xiayan/bin/svtoolkit/conf/genstrip_parameters.txt INFO 17:49:29,335 HelpFormatter - Executing as xiayan@localhost.localdomain on Linux 2.6.32-431.3.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_45-mockbuild_2013_11_22_18_30-b00. INFO 17:49:29,336 HelpFormatter - Date/Time: 2015/05/08 17:49:29 INFO 17:49:29,336 HelpFormatter - ---------------------------------------------------------- INFO 17:49:29,336 HelpFormatter - ---------------------------------------------------------- INFO 17:49:29,355 MetaData - Opening metadata ... INFO 17:49:29,355 MetaData - Adding metadata directory /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata ... INFO 17:49:29,356 MetaData - Opened metadata. INFO 17:49:29,357 ComputeGCProfiles - Opening reference sequence ... INFO 17:49:29,358 ComputeGCProfiles - Opened reference sequence. INFO 17:49:29,358 ComputeGCProfiles - Opening genome mask ... INFO 17:49:29,359 ComputeGCProfiles - Opened genome mask. INFO 17:49:29,360 ComputeGCProfiles - Opening copy number mask ... INFO 17:49:29,360 ComputeGCProfiles - Opened copy number mask. INFO 17:49:29,360 ComputeGCProfiles - Initializing algorithm ... #INFO: ReadCountAlgorithm: detected metadata version 1, forcing legacy behavior INFO 17:49:29,364 ComputeGCProfiles - Algorithm initialized. INFO 17:49:29,364 ComputeGCProfiles - Computing reference GC profile ... #DBG: Fri May 08 17:49:29 CST 2015 computing reference profile for the interval Chr01:1-73727935 #DBG: Fri May 08 17:49:41 CST 2015 computing reference profile for the interval Chr02:1-77694824 #DBG: Fri May 08 17:49:54 CST 2015 computing reference profile for the interval Chr03:1-74408397 #DBG: Fri May 08 17:50:06 CST 2015 computing reference profile for the interval Chr04:1-67966759 #DBG: Fri May 08 17:50:17 CST 2015 computing reference profile for the interval Chr05:1-62243505 #DBG: Fri May 08 17:50:27 CST 2015 computing reference profile for the interval Chr06:1-62192017 #DBG: Fri May 08 17:50:38 CST 2015 computing reference profile for the interval Chr07:1-64263908 #DBG: Fri May 08 17:50:48 CST 2015 computing reference profile for the interval Chr08:1-55354556 #DBG: Fri May 08 17:50:57 CST 2015 computing reference profile for the interval Chr09:1-59454246 #DBG: Fri May 08 17:51:07 CST 2015 computing reference profile for the interval Chr10:1-61085274 #DBG: Fri May 08 17:51:17 CST 2015 computing reference profile for the interval super_10:1-8818317 Exception in thread "main" java.lang.RuntimeException: Invalid sequence position: super_10:746 at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:61) 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.commandline.CommandLineProgram.run(CommandLineProgram.java:25) at org.broadinstitute.sv.apps.ComputeGCProfiles.main(ComputeGCProfiles.java:125) Caused by: java.lang.IllegalArgumentException: Invalid sequence position: super_10:746 at org.broadinstitute.sv.mask.GenomeMaskFastaFile.getMaskBit(GenomeMaskFastaFile.java:80) at org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeIntervalProfile(GCProfileAlgorithm.java:338) at org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeReferenceProfileMap(GCProfileAlgorithm.java:225) at org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeReferenceProfile(GCProfileAlgorithm.java:181) at org.broadinstitute.sv.apps.ComputeGCProfiles.run(ComputeGCProfiles.java:172) at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:50) ... 4 more INFO 17:51:17,286 QGraph - Writing incremental jobs reports... INFO 17:51:17,286 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 17:51:17,686 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB1/SB1.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB1.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 17:51:17,686 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-6.out INFO 18:00:30,522 QGraph - 6741 Pend, 1 Run, 1 Fail, 4 Done INFO 18:00:30,525 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB1/SB1.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB1.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:00:30,527 QGraph - Writing incremental jobs reports... INFO 18:00:30,527 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 18:00:30,937 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB2/SB2.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB2.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:00:30,938 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-7.out INFO 18:12:40,946 QGraph - 6740 Pend, 1 Run, 1 Fail, 5 Done INFO 18:12:40,949 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB2/SB2.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB2.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:12:40,950 QGraph - Writing incremental jobs reports... INFO 18:12:40,951 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 18:12:41,344 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB3/SB3.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB3.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:12:41,344 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-8.out INFO 18:16:33,033 QGraph - 6739 Pend, 1 Run, 1 Fail, 6 Done INFO 18:16:33,035 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB3/SB3.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB3.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:16:33,036 QGraph - Writing incremental jobs reports... INFO 18:16:33,036 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 18:16:33,434 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB4/SB4.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB4.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:16:33,434 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-9.out INFO 18:20:49,007 QGraph - 6738 Pend, 1 Run, 1 Fail, 7 Done INFO 18:20:49,009 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB4/SB4.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB4.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:20:49,009 QGraph - Writing incremental jobs reports... INFO 18:20:49,009 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 18:20:49,405 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB5/SB5.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB5.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:20:49,405 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-10.out INFO 18:31:30,220 QGraph - 6737 Pend, 1 Run, 1 Fail, 8 Done INFO 18:31:30,222 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB5/SB5.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB5.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:31:30,223 QGraph - Writing incremental jobs reports... INFO 18:31:30,223 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 18:31:30,684 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB6/SB6.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB6.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:31:30,684 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-11.out INFO 18:41:34,111 QGraph - 6736 Pend, 1 Run, 1 Fail, 9 Done INFO 18:41:34,113 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB6/SB6.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB6.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:41:34,114 QGraph - Writing incremental jobs reports... INFO 18:41:34,114 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 18:41:34,462 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB7/SB7.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB7.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:41:34,463 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-12.out INFO 18:45:30,399 QGraph - 6735 Pend, 1 Run, 1 Fail, 10 Done INFO 18:45:30,401 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB7/SB7.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB7.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:45:30,402 QGraph - Writing incremental jobs reports... INFO 18:45:30,402 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 18:45:30,746 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB8/SB8.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB8.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:45:30,746 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-13.out INFO 18:49:39,981 QGraph - 6734 Pend, 1 Run, 1 Fail, 11 Done INFO 18:49:39,983 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB8/SB8.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB8.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:49:39,983 QGraph - Writing incremental jobs reports... INFO 18:49:39,983 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 18:49:40,338 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB9/SB9.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB9.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:49:40,338 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-14.out INFO 18:53:18,644 QGraph - 6733 Pend, 1 Run, 1 Fail, 12 Done INFO 18:53:18,645 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB9/SB9.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB9.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:53:18,645 QGraph - Writing incremental jobs reports... INFO 18:53:18,645 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 18:53:19,004 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB10/SB10.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB10.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:53:19,004 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-15.out INFO 18:57:16,078 QGraph - 6732 Pend, 1 Run, 1 Fail, 13 Done INFO 18:57:16,086 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB10/SB10.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB10.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:57:16,087 QGraph - Writing incremental jobs reports... INFO 18:57:16,087 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 18:57:16,438 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB11/SB11.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB11.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 18:57:16,439 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-16.out INFO 19:08:13,755 QGraph - 6731 Pend, 1 Run, 1 Fail, 14 Done INFO 19:08:13,757 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB11/SB11.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB11.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:08:13,757 QGraph - Writing incremental jobs reports... INFO 19:08:13,758 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:08:14,102 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB12/SB12.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB12.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:08:14,102 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-17.out INFO 19:11:31,712 QGraph - 6730 Pend, 1 Run, 1 Fail, 15 Done INFO 19:11:31,715 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB12/SB12.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB12.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:11:31,715 QGraph - Writing incremental jobs reports... INFO 19:11:31,715 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:11:32,070 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB13/SB13.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB13.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:11:32,070 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-18.out INFO 19:17:36,088 QGraph - 6729 Pend, 1 Run, 1 Fail, 16 Done INFO 19:17:36,090 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB13/SB13.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB13.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:17:36,090 QGraph - Writing incremental jobs reports... INFO 19:17:36,091 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:17:36,442 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB14/SB14.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB14.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:17:36,443 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-19.out INFO 19:20:33,494 QGraph - 6728 Pend, 1 Run, 1 Fail, 17 Done INFO 19:20:33,504 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB14/SB14.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB14.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:20:33,504 QGraph - Writing incremental jobs reports... INFO 19:20:33,504 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:20:33,868 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB15/SB15.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB15.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:20:33,868 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-20.out INFO 19:25:05,540 QGraph - 6727 Pend, 1 Run, 1 Fail, 18 Done INFO 19:25:05,542 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB15/SB15.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB15.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:25:05,543 QGraph - Writing incremental jobs reports... INFO 19:25:05,543 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:25:05,895 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB16/SB16.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB16.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:25:05,896 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-21.out INFO 19:27:14,659 QGraph - 6726 Pend, 1 Run, 1 Fail, 19 Done INFO 19:27:14,661 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB16/SB16.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB16.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:27:14,661 QGraph - Writing incremental jobs reports... INFO 19:27:14,661 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:27:15,028 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB17/SB17.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB17.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:27:15,028 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-22.out INFO 19:31:00,382 QGraph - 6725 Pend, 1 Run, 1 Fail, 20 Done INFO 19:31:00,384 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB17/SB17.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB17.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:31:00,384 QGraph - Writing incremental jobs reports... INFO 19:31:00,384 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:31:00,824 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB18/SB18.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB18.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:31:00,824 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-23.out INFO 19:33:25,618 QGraph - 6724 Pend, 1 Run, 1 Fail, 21 Done INFO 19:33:25,619 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB18/SB18.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB18.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:33:25,620 QGraph - Writing incremental jobs reports... INFO 19:33:25,620 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:33:25,991 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB19/SB19.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB19.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:33:25,991 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-24.out INFO 19:38:04,544 QGraph - 6723 Pend, 1 Run, 1 Fail, 22 Done INFO 19:38:04,546 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB19/SB19.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB19.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:38:04,546 QGraph - Writing incremental jobs reports... INFO 19:38:04,546 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:38:04,904 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB20/SB20.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB20.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:38:04,904 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-25.out INFO 19:42:43,781 QGraph - 6722 Pend, 1 Run, 1 Fail, 23 Done INFO 19:42:43,783 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB20/SB20.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB20.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:42:43,783 QGraph - Writing incremental jobs reports... INFO 19:42:43,783 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:42:44,148 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB21/SB21.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB21.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:42:44,148 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-26.out INFO 19:45:18,518 QGraph - 6721 Pend, 1 Run, 1 Fail, 24 Done INFO 19:45:18,520 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB21/SB21.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB21.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:45:18,520 QGraph - Writing incremental jobs reports... INFO 19:45:18,521 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:45:18,877 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB22/SB22.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB22.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:45:18,877 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-27.out INFO 19:49:47,233 QGraph - 6720 Pend, 1 Run, 1 Fail, 25 Done INFO 19:49:47,235 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB22/SB22.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB22.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:49:47,236 QGraph - Writing incremental jobs reports... INFO 19:49:47,236 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:49:47,583 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB23/SB23.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB23.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:49:47,584 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-28.out INFO 19:52:05,120 QGraph - 6719 Pend, 1 Run, 1 Fail, 26 Done INFO 19:52:05,122 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB23/SB23.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB23.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:52:05,122 QGraph - Writing incremental jobs reports... INFO 19:52:05,123 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:52:05,487 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB24/SB24.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB24.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:52:05,487 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-29.out INFO 19:56:19,460 QGraph - 6718 Pend, 1 Run, 1 Fail, 27 Done INFO 19:56:19,462 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB24/SB24.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB24.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:56:19,462 QGraph - Writing incremental jobs reports... INFO 19:56:19,462 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:56:19,825 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB25/SB25.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB25.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:56:19,825 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-30.out INFO 19:59:28,020 QGraph - 6717 Pend, 1 Run, 1 Fail, 28 Done INFO 19:59:28,022 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB25/SB25.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB25.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:59:28,022 QGraph - Writing incremental jobs reports... INFO 19:59:28,023 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 19:59:28,377 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB26/SB26.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB26.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 19:59:28,377 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-31.out INFO 20:01:41,045 QGraph - 6716 Pend, 1 Run, 1 Fail, 29 Done INFO 20:01:41,046 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB26/SB26.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB26.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 20:01:41,047 QGraph - Writing incremental jobs reports... INFO 20:01:41,047 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:01:41,422 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB27/SB27.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB27.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 20:01:41,423 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-32.out INFO 20:04:44,687 QGraph - 6715 Pend, 1 Run, 1 Fail, 30 Done INFO 20:04:44,689 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB27/SB27.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB27.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 20:04:44,689 QGraph - Writing incremental jobs reports... INFO 20:04:44,689 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:04:45,035 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB28/SB28.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB28.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 20:04:45,036 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-33.out INFO 20:09:32,862 QGraph - 6714 Pend, 1 Run, 1 Fail, 31 Done INFO 20:09:32,864 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB28/SB28.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB28.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 20:09:32,864 QGraph - Writing incremental jobs reports... INFO 20:09:32,864 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:09:33,220 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeInsertSizeHistograms' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB1.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB2.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB3.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB4.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB5.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB6.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB7.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB8.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB9.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB10.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB11.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB12.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB13.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB14.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB15.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB16.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB17.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB18.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB19.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB20.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB21.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB22.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB23.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB24.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB25.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB26.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB27.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB28.realn.hist.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.hist.bin' INFO 20:09:33,221 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-34.out INFO 20:09:41,275 QGraph - 6713 Pend, 1 Run, 1 Fail, 32 Done INFO 20:10:02,865 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeInsertSizeHistograms' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB1.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB2.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB3.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB4.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB5.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB6.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB7.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB8.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB9.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB10.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB11.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB12.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB13.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB14.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB15.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB16.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB17.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB18.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB19.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB20.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB21.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB22.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB23.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB24.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB25.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB26.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB27.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB28.realn.hist.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.hist.bin' INFO 20:10:02,865 QGraph - Writing incremental jobs reports... INFO 20:10:02,866 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:10:03,237 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.hist.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.dist.bin' INFO 20:10:03,237 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-35.out INFO 20:11:35,246 QGraph - 6712 Pend, 1 Run, 1 Fail, 33 Done INFO 20:11:35,248 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.hist.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.dist.bin' INFO 20:11:35,249 QGraph - Writing incremental jobs reports... INFO 20:11:35,249 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:11:35,611 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeInsertStatistics' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.dist.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.stats.dat' INFO 20:11:35,611 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-36.out INFO 20:11:40,918 QGraph - 6711 Pend, 1 Run, 1 Fail, 34 Done INFO 20:12:05,248 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeInsertStatistics' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.dist.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.stats.dat' INFO 20:12:05,249 QGraph - Writing incremental jobs reports... INFO 20:12:05,249 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:12:05,624 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB1/SB1.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB1.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 20:12:05,624 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-37.out INFO 20:19:26,830 QGraph - 6710 Pend, 1 Run, 1 Fail, 35 Done INFO 20:19:26,836 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB1/SB1.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB1.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 20:19:26,837 QGraph - Writing incremental jobs reports... INFO 20:19:26,837 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:19:27,208 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB2/SB2.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB2.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 20:19:27,209 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-38.out INFO 20:29:56,832 QGraph - 6709 Pend, 1 Run, 1 Fail, 36 Done INFO 20:29:56,841 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB2/SB2.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB2.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 20:29:56,842 QGraph - Writing incremental jobs reports... INFO 20:29:56,842 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:29:57,251 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB3/SB3.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB3.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 20:29:57,252 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-39.out INFO 20:33:51,360 QGraph - 6708 Pend, 1 Run, 1 Fail, 37 Done INFO 20:33:51,362 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB3/SB3.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB3.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 20:33:51,362 QGraph - Writing incremental jobs reports... INFO 20:33:51,362 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:33:51,731 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB4/SB4.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB4.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 20:33:51,731 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-40.out INFO 20:35:48,831 QCommandLine - Shutting down jobs. Please wait... INFO 20:35:48,844 QGraph - 6707 Pend, 1 Run, 1 Fail, 38 Done ERROR 20:35:48,848 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB4/SB4.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB4.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' ERROR 20:35:48,848 FunctionEdge - Contents of /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-40.out: INFO 20:33:57,492 HelpFormatter - --------------------------------------------------------------------------- INFO 20:33:57,495 HelpFormatter - The Genome Analysis Toolkit (GATK) v, Compiled 2015/03/15 21:58:08 INFO 20:33:57,495 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 20:33:57,495 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 20:33:57,502 HelpFormatter - Program Args: -T ComputeReadDepthCoverageWalker -R /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta -O /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB4.realn.depth.txt -disableGATKTraversal true -md /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata -ploidyMapFile /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt -genomeMaskFile /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta -readDepthMaskFile /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed -minMapQ 10 -insertSizeRadius 10.0 INFO 20:33:57,510 HelpFormatter - Executing as xiayan@localhost.localdomain on Linux 2.6.32-431.3.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_45-mockbuild_2013_11_22_18_30-b00. INFO 20:33:57,510 HelpFormatter - Date/Time: 2015/05/08 20:33:57 INFO 20:33:57,510 HelpFormatter - --------------------------------------------------------------------------- INFO 20:33:57,511 HelpFormatter - --------------------------------------------------------------------------- INFO 20:33:57,605 GenomeAnalysisEngine - Strictness is SILENT INFO 20:33:57,887 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 20:33:58,002 GenomeAnalysisEngine - Preparing for traversal INFO 20:33:58,051 GenomeAnalysisEngine - Done preparing for traversal INFO 20:33:58,051 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 20:33:58,051 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 20:33:58,051 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime INFO 20:33:58,053 MetaData - Opening metadata ... INFO 20:33:58,053 MetaData - Adding metadata directory /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata ... INFO 20:33:58,054 MetaData - Opened metadata. #INFO: ReadCountAlgorithm: detected metadata version 1, forcing legacy behavior INFO 20:33:58,172 MetaData - Loading insert size distributions ... INFO 20:33:58,222 ComputeReadDepthCoverageWalker - Using genome mask /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta INFO 20:34:28,061 ProgressMeter - Starting 0.0 30.0 s 49.6 w 100.0% 30.0 s 0.0 s INFO 20:34:58,064 ProgressMeter - Starting 0.0 60.0 s 99.2 w 100.0% 60.0 s 0.0 s INFO 20:35:28,065 ProgressMeter - Starting 0.0 90.0 s 148.8 w 100.0% 90.0 s 0.0 s INFO 20:35:48,849 QGraph - Writing incremental jobs reports... INFO 20:35:48,849 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:35:49,211 QGraph - 6707 Pend, 0 Run, 2 Fail, 38 Done INFO 20:35:49,219 QCommandLine - Writing final jobs report... INFO 20:35:49,219 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:39:08,140 QScriptManager - Compiling 2 QScripts INFO 20:39:21,934 QScriptManager - Compilation complete INFO 20:39:22,034 HelpFormatter - ---------------------------------------------------------------------- INFO 20:39:22,034 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/03/15 21:58:08 INFO 20:39:22,034 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 20:39:22,034 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 20:39:22,035 HelpFormatter - Program Args: -S /disk/disk1/work/xiayan/bin/svtoolkit/qscript/SVPreprocess.q -S /disk/disk1/work/xiayan/bin/svtoolkit/qscript/SVQScript.q -cp /disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar -gatk /disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -configFile /disk/disk1/work/xiayan/bin/svtoolkit/conf/genstrip_parameters.txt -tempDir /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR -R /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/population.list -md /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata -runDirectory /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1 -useMultiStep -reduceInsertSizeDistributions true -computeReadCounts true -jobLogDir /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs -computeGCProfiles true -jobRunner Shell -gatkJobRunner Shell -run INFO 20:39:22,035 HelpFormatter - Executing as xiayan@localhost.localdomain on Linux 2.6.32-431.3.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_45-mockbuild_2013_11_22_18_30-b00. INFO 20:39:22,036 HelpFormatter - Date/Time: 2015/05/08 20:39:22 INFO 20:39:22,036 HelpFormatter - ---------------------------------------------------------------------- INFO 20:39:22,036 HelpFormatter - ---------------------------------------------------------------------- INFO 20:39:22,044 QCommandLine - Scripting SVPreprocess INFO 20:39:27,118 QCommandLine - Added 6747 functions INFO 20:39:27,118 QGraph - Generating graph. INFO 20:39:27,874 QGraph - Running jobs. INFO 20:39:29,540 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/gcprofile/reference.gcprof.zip' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-writeReferenceProfile' 'true' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-copyNumberMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.gcmask.fasta' '-configFile' '/disk/disk1/work/xiayan/bin/svtoolkit/conf/genstrip_parameters.txt' INFO 20:39:29,540 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-5.out INFO 20:41:30,142 QGraph - 6742 Pend, 1 Run, 0 Fail, 4 Done ERROR 20:41:30,151 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/gcprofile/reference.gcprof.zip' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-writeReferenceProfile' 'true' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-copyNumberMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.gcmask.fasta' '-configFile' '/disk/disk1/work/xiayan/bin/svtoolkit/conf/genstrip_parameters.txt' ERROR 20:41:30,155 FunctionEdge - Contents of /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-5.out: INFO 20:39:35,386 HelpFormatter - ---------------------------------------------------------- INFO 20:39:35,389 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ComputeGCProfiles INFO 20:39:35,396 HelpFormatter - Program Args: -O /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/gcprofile/reference.gcprof.zip -R /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta -md /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata -writeReferenceProfile true -genomeMaskFile /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta -copyNumberMaskFile /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.gcmask.fasta -configFile /disk/disk1/work/xiayan/bin/svtoolkit/conf/genstrip_parameters.txt INFO 20:39:35,404 HelpFormatter - Executing as xiayan@localhost.localdomain on Linux 2.6.32-431.3.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_45-mockbuild_2013_11_22_18_30-b00. INFO 20:39:35,405 HelpFormatter - Date/Time: 2015/05/08 20:39:35 INFO 20:39:35,405 HelpFormatter - ---------------------------------------------------------- INFO 20:39:35,406 HelpFormatter - ---------------------------------------------------------- INFO 20:39:35,433 MetaData - Opening metadata ... INFO 20:39:35,433 MetaData - Adding metadata directory /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata ... INFO 20:39:35,434 MetaData - Opened metadata. INFO 20:39:35,434 ComputeGCProfiles - Opening reference sequence ... INFO 20:39:35,436 ComputeGCProfiles - Opened reference sequence. INFO 20:39:35,436 ComputeGCProfiles - Opening genome mask ... INFO 20:39:35,437 ComputeGCProfiles - Opened genome mask. INFO 20:39:35,437 ComputeGCProfiles - Opening copy number mask ... INFO 20:39:35,438 ComputeGCProfiles - Opened copy number mask. INFO 20:39:35,438 ComputeGCProfiles - Initializing algorithm ... #INFO: ReadCountAlgorithm: detected metadata version 1, forcing legacy behavior INFO 20:39:35,442 ComputeGCProfiles - Algorithm initialized. INFO 20:39:35,442 ComputeGCProfiles - Computing reference GC profile ... #DBG: Fri May 08 20:39:35 CST 2015 computing reference profile for the interval Chr01:1-73727935 #DBG: Fri May 08 20:39:49 CST 2015 computing reference profile for the interval Chr02:1-77694824 #DBG: Fri May 08 20:40:02 CST 2015 computing reference profile for the interval Chr03:1-74408397 #DBG: Fri May 08 20:40:15 CST 2015 computing reference profile for the interval Chr04:1-67966759 #DBG: Fri May 08 20:40:27 CST 2015 computing reference profile for the interval Chr05:1-62243505 #DBG: Fri May 08 20:40:37 CST 2015 computing reference profile for the interval Chr06:1-62192017 #DBG: Fri May 08 20:40:48 CST 2015 computing reference profile for the interval Chr07:1-64263908 #DBG: Fri May 08 20:40:59 CST 2015 computing reference profile for the interval Chr08:1-55354556 #DBG: Fri May 08 20:41:08 CST 2015 computing reference profile for the interval Chr09:1-59454246 #DBG: Fri May 08 20:41:19 CST 2015 computing reference profile for the interval Chr10:1-61085274 #DBG: Fri May 08 20:41:30 CST 2015 computing reference profile for the interval super_10:1-8818317 Exception in thread "main" java.lang.RuntimeException: Invalid sequence position: super_10:746 at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:61) 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.commandline.CommandLineProgram.run(CommandLineProgram.java:25) at org.broadinstitute.sv.apps.ComputeGCProfiles.main(ComputeGCProfiles.java:125) Caused by: java.lang.IllegalArgumentException: Invalid sequence position: super_10:746 at org.broadinstitute.sv.mask.GenomeMaskFastaFile.getMaskBit(GenomeMaskFastaFile.java:80) at org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeIntervalProfile(GCProfileAlgorithm.java:338) at org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeReferenceProfileMap(GCProfileAlgorithm.java:225) at org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeReferenceProfile(GCProfileAlgorithm.java:181) at org.broadinstitute.sv.apps.ComputeGCProfiles.run(ComputeGCProfiles.java:172) at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:50) ... 4 more INFO 20:41:30,157 QGraph - Writing incremental jobs reports... INFO 20:41:30,157 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:41:30,555 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB1/SB1.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB1.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 20:41:30,555 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-6.out INFO 20:49:45,282 QGraph - 6741 Pend, 1 Run, 1 Fail, 4 Done INFO 20:49:45,293 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB1/SB1.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB1.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 20:49:45,294 QGraph - Writing incremental jobs reports... INFO 20:49:45,294 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 20:49:45,688 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB2/SB2.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB2.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 20:49:45,688 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-7.out INFO 21:02:32,541 QGraph - 6740 Pend, 1 Run, 1 Fail, 5 Done INFO 21:02:32,551 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB2/SB2.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB2.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:02:32,552 QGraph - Writing incremental jobs reports... INFO 21:02:32,552 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 21:02:32,947 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB3/SB3.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB3.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:02:32,947 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-8.out INFO 21:06:53,602 QGraph - 6739 Pend, 1 Run, 1 Fail, 6 Done INFO 21:06:53,604 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB3/SB3.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB3.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:06:53,605 QGraph - Writing incremental jobs reports... INFO 21:06:53,605 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 21:06:54,038 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB4/SB4.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB4.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:06:54,038 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-9.out INFO 21:10:48,540 QGraph - 6738 Pend, 1 Run, 1 Fail, 7 Done INFO 21:10:48,543 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB4/SB4.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB4.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:10:48,543 QGraph - Writing incremental jobs reports... INFO 21:10:48,543 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 21:10:48,953 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB5/SB5.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB5.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:10:48,953 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-10.out INFO 21:21:11,297 QGraph - 6737 Pend, 1 Run, 1 Fail, 8 Done INFO 21:21:11,299 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB5/SB5.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB5.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:21:11,300 QGraph - Writing incremental jobs reports... INFO 21:21:11,301 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 21:21:11,758 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB6/SB6.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB6.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:21:11,758 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-11.out INFO 21:30:56,167 QGraph - 6736 Pend, 1 Run, 1 Fail, 9 Done INFO 21:30:56,169 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB6/SB6.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB6.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:30:56,170 QGraph - Writing incremental jobs reports... INFO 21:30:56,170 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 21:30:56,533 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB7/SB7.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB7.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:30:56,533 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-12.out INFO 21:34:27,843 QGraph - 6735 Pend, 1 Run, 1 Fail, 10 Done INFO 21:34:27,853 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB7/SB7.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB7.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:34:27,854 QGraph - Writing incremental jobs reports... INFO 21:34:27,854 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 21:34:28,202 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB8/SB8.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB8.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:34:28,202 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-13.out INFO 21:38:42,695 QGraph - 6734 Pend, 1 Run, 1 Fail, 11 Done INFO 21:38:42,704 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB8/SB8.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB8.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:38:42,705 QGraph - Writing incremental jobs reports... INFO 21:38:42,705 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 21:38:43,067 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB9/SB9.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB9.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:38:43,067 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-14.out INFO 21:42:14,162 QGraph - 6733 Pend, 1 Run, 1 Fail, 12 Done INFO 21:42:14,171 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB9/SB9.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB9.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:42:14,172 QGraph - Writing incremental jobs reports... INFO 21:42:14,172 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 21:42:14,532 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB10/SB10.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB10.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:42:14,533 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-15.out INFO 21:46:08,388 QGraph - 6732 Pend, 1 Run, 1 Fail, 13 Done INFO 21:46:08,397 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB10/SB10.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB10.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:46:08,397 QGraph - Writing incremental jobs reports... INFO 21:46:08,397 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 21:46:08,730 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB11/SB11.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB11.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:46:08,730 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-16.out INFO 21:57:21,937 QGraph - 6731 Pend, 1 Run, 1 Fail, 14 Done INFO 21:57:21,947 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB11/SB11.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB11.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:57:21,947 QGraph - Writing incremental jobs reports... INFO 21:57:21,947 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 21:57:22,309 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB12/SB12.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB12.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 21:57:22,309 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-17.out INFO 22:00:57,992 QGraph - 6730 Pend, 1 Run, 1 Fail, 15 Done INFO 22:00:57,994 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB12/SB12.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB12.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:00:57,994 QGraph - Writing incremental jobs reports... INFO 22:00:57,995 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:00:58,355 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB13/SB13.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB13.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:00:58,356 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-18.out INFO 22:06:33,805 QGraph - 6729 Pend, 1 Run, 1 Fail, 16 Done INFO 22:06:33,814 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB13/SB13.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB13.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:06:33,814 QGraph - Writing incremental jobs reports... INFO 22:06:33,814 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:06:34,170 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB14/SB14.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB14.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:06:34,170 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-19.out INFO 22:09:30,643 QGraph - 6728 Pend, 1 Run, 1 Fail, 17 Done INFO 22:09:30,653 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB14/SB14.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB14.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:09:30,654 QGraph - Writing incremental jobs reports... INFO 22:09:30,654 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:09:31,024 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB15/SB15.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB15.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:09:31,024 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-20.out INFO 22:14:37,406 QGraph - 6727 Pend, 1 Run, 1 Fail, 18 Done INFO 22:14:37,415 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB15/SB15.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB15.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:14:37,415 QGraph - Writing incremental jobs reports... INFO 22:14:37,415 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:14:37,764 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB16/SB16.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB16.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:14:37,764 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-21.out INFO 22:17:00,441 QGraph - 6726 Pend, 1 Run, 1 Fail, 19 Done INFO 22:17:00,443 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB16/SB16.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB16.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:17:00,443 QGraph - Writing incremental jobs reports... INFO 22:17:00,444 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:17:00,806 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB17/SB17.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB17.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:17:00,806 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-22.out INFO 22:21:07,964 QGraph - 6725 Pend, 1 Run, 1 Fail, 20 Done INFO 22:21:07,965 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB17/SB17.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB17.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:21:07,966 QGraph - Writing incremental jobs reports... INFO 22:21:07,966 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:21:08,397 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB18/SB18.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB18.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:21:08,398 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-23.out INFO 22:23:29,052 QGraph - 6724 Pend, 1 Run, 1 Fail, 21 Done INFO 22:23:29,053 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB18/SB18.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB18.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:23:29,054 QGraph - Writing incremental jobs reports... INFO 22:23:29,054 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:23:29,437 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB19/SB19.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB19.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:23:29,438 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-24.out INFO 22:28:03,259 QGraph - 6723 Pend, 1 Run, 1 Fail, 22 Done INFO 22:28:03,261 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB19/SB19.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB19.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:28:03,261 QGraph - Writing incremental jobs reports... INFO 22:28:03,261 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:28:03,630 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB20/SB20.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB20.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:28:03,630 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-25.out INFO 22:32:40,760 QGraph - 6722 Pend, 1 Run, 1 Fail, 23 Done INFO 22:32:40,762 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB20/SB20.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB20.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:32:40,762 QGraph - Writing incremental jobs reports... INFO 22:32:40,762 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:32:41,117 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB21/SB21.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB21.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:32:41,117 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-26.out INFO 22:35:15,182 QGraph - 6721 Pend, 1 Run, 1 Fail, 24 Done INFO 22:35:15,184 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB21/SB21.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB21.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:35:15,185 QGraph - Writing incremental jobs reports... INFO 22:35:15,185 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:35:15,538 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB22/SB22.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB22.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:35:15,539 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-27.out INFO 22:39:11,793 QGraph - 6720 Pend, 1 Run, 1 Fail, 25 Done INFO 22:39:11,795 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB22/SB22.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB22.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:39:11,796 QGraph - Writing incremental jobs reports... INFO 22:39:11,796 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:39:12,150 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB23/SB23.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB23.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:39:12,150 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-28.out INFO 22:41:26,363 QGraph - 6719 Pend, 1 Run, 1 Fail, 26 Done INFO 22:41:26,365 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB23/SB23.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB23.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:41:26,365 QGraph - Writing incremental jobs reports... INFO 22:41:26,365 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:41:26,724 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB24/SB24.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB24.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:41:26,725 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-29.out INFO 22:45:18,159 QGraph - 6718 Pend, 1 Run, 1 Fail, 27 Done INFO 22:45:18,161 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB24/SB24.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB24.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:45:18,161 QGraph - Writing incremental jobs reports... INFO 22:45:18,162 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:45:18,528 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB25/SB25.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB25.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:45:18,528 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-30.out INFO 22:48:26,259 QGraph - 6717 Pend, 1 Run, 1 Fail, 28 Done INFO 22:48:26,261 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB25/SB25.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB25.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:48:26,261 QGraph - Writing incremental jobs reports... INFO 22:48:26,262 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:48:26,630 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB26/SB26.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB26.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:48:26,631 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-31.out INFO 22:50:29,587 QGraph - 6716 Pend, 1 Run, 1 Fail, 29 Done INFO 22:50:29,589 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB26/SB26.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB26.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:50:29,589 QGraph - Writing incremental jobs reports... INFO 22:50:29,589 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:50:29,947 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB27/SB27.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB27.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:50:29,947 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-32.out INFO 22:53:04,219 QGraph - 6715 Pend, 1 Run, 1 Fail, 30 Done INFO 22:53:04,221 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB27/SB27.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB27.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:53:04,221 QGraph - Writing incremental jobs reports... INFO 22:53:04,222 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:53:04,584 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB28/SB28.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB28.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:53:04,584 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-33.out INFO 22:57:28,370 QGraph - 6714 Pend, 1 Run, 1 Fail, 31 Done INFO 22:57:28,372 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB28/SB28.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB28.realn.hist.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' -createEmpty INFO 22:57:28,372 QGraph - Writing incremental jobs reports... INFO 22:57:28,372 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:57:28,745 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeInsertSizeHistograms' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB1.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB2.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB3.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB4.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB5.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB6.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB7.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB8.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB9.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB10.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB11.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB12.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB13.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB14.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB15.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB16.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB17.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB18.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB19.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB20.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB21.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB22.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB23.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB24.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB25.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB26.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB27.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB28.realn.hist.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.hist.bin' INFO 22:57:28,745 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-34.out INFO 22:57:36,411 QGraph - 6713 Pend, 1 Run, 1 Fail, 32 Done INFO 22:57:58,373 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeInsertSizeHistograms' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB1.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB2.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB3.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB4.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB5.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB6.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB7.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB8.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB9.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB10.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB11.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB12.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB13.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB14.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB15.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB16.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB17.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB18.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB19.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB20.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB21.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB22.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB23.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB24.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB25.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB26.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB27.realn.hist.bin' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd/SB28.realn.hist.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.hist.bin' INFO 22:57:58,373 QGraph - Writing incremental jobs reports... INFO 22:57:58,374 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:57:58,726 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.hist.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.dist.bin' INFO 22:57:58,726 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-35.out INFO 22:59:25,441 QGraph - 6712 Pend, 1 Run, 1 Fail, 33 Done INFO 22:59:25,443 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.hist.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.dist.bin' INFO 22:59:25,444 QGraph - Writing incremental jobs reports... INFO 22:59:25,444 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:59:25,807 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeInsertStatistics' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.dist.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.stats.dat' INFO 22:59:25,807 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-36.out INFO 22:59:30,808 QGraph - 6711 Pend, 1 Run, 1 Fail, 34 Done INFO 22:59:55,443 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeInsertStatistics' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.dist.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/isd.stats.dat' INFO 22:59:55,443 QGraph - Writing incremental jobs reports... INFO 22:59:55,444 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 22:59:55,829 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB1/SB1.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB1.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 22:59:55,829 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-37.out INFO 23:07:42,507 QGraph - 6710 Pend, 1 Run, 1 Fail, 35 Done INFO 23:07:42,509 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB1/SB1.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB1.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:07:42,510 QGraph - Writing incremental jobs reports... INFO 23:07:42,510 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 23:07:42,892 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB2/SB2.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB2.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:07:42,893 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-38.out INFO 23:18:29,277 QGraph - 6709 Pend, 1 Run, 1 Fail, 36 Done INFO 23:18:29,318 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB2/SB2.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB2.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:18:29,319 QGraph - Writing incremental jobs reports... INFO 23:18:29,319 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 23:18:29,714 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB3/SB3.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB3.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:18:29,714 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-39.out INFO 23:22:19,423 QGraph - 6708 Pend, 1 Run, 1 Fail, 37 Done INFO 23:22:19,426 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB3/SB3.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB3.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:22:19,426 QGraph - Writing incremental jobs reports... INFO 23:22:19,427 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 23:22:19,821 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB4/SB4.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB4.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:22:19,821 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-40.out INFO 23:26:10,702 QGraph - 6707 Pend, 1 Run, 1 Fail, 38 Done INFO 23:26:10,704 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB4/SB4.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB4.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:26:10,705 QGraph - Writing incremental jobs reports... INFO 23:26:10,705 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 23:26:11,094 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB5/SB5.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB5.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:26:11,095 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-41.out INFO 23:35:02,156 QGraph - 6706 Pend, 1 Run, 1 Fail, 39 Done INFO 23:35:02,158 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB5/SB5.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB5.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:35:02,159 QGraph - Writing incremental jobs reports... INFO 23:35:02,159 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 23:35:02,581 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB6/SB6.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB6.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:35:02,581 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-42.out INFO 23:43:19,152 QGraph - 6705 Pend, 1 Run, 1 Fail, 40 Done INFO 23:43:19,154 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB6/SB6.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB6.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:43:19,154 QGraph - Writing incremental jobs reports... INFO 23:43:19,154 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 23:43:19,556 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB7/SB7.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB7.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:43:19,557 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-43.out INFO 23:46:32,364 QGraph - 6704 Pend, 1 Run, 1 Fail, 41 Done INFO 23:46:32,365 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB7/SB7.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB7.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:46:32,366 QGraph - Writing incremental jobs reports... INFO 23:46:32,366 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 23:46:32,756 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB8/SB8.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB8.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:46:32,756 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-44.out INFO 23:50:19,763 QGraph - 6703 Pend, 1 Run, 1 Fail, 42 Done INFO 23:50:19,765 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB8/SB8.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB8.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:50:19,766 QGraph - Writing incremental jobs reports... INFO 23:50:19,766 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 23:50:20,171 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB9/SB9.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB9.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:50:20,171 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-45.out INFO 23:54:05,545 QGraph - 6702 Pend, 1 Run, 1 Fail, 43 Done INFO 23:54:05,546 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB9/SB9.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB9.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:54:05,547 QGraph - Writing incremental jobs reports... INFO 23:54:05,547 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 23:54:05,977 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB10/SB10.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB10.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:54:05,977 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-46.out INFO 23:58:06,635 QGraph - 6701 Pend, 1 Run, 1 Fail, 44 Done INFO 23:58:06,637 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB10/SB10.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB10.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:58:06,637 QGraph - Writing incremental jobs reports... INFO 23:58:06,638 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 23:58:07,018 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB11/SB11.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB11.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 23:58:07,018 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-47.out INFO 00:07:48,640 QGraph - 6700 Pend, 1 Run, 1 Fail, 45 Done INFO 00:07:48,642 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB11/SB11.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB11.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:07:48,642 QGraph - Writing incremental jobs reports... INFO 00:07:48,643 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:07:49,013 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB12/SB12.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB12.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:07:49,013 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-48.out INFO 00:10:51,161 QGraph - 6699 Pend, 1 Run, 1 Fail, 46 Done INFO 00:10:51,170 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB12/SB12.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB12.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:10:51,171 QGraph - Writing incremental jobs reports... INFO 00:10:51,171 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:10:51,523 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB13/SB13.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB13.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:10:51,523 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-49.out INFO 00:16:17,791 QGraph - 6698 Pend, 1 Run, 1 Fail, 47 Done INFO 00:16:17,793 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB13/SB13.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB13.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:16:17,793 QGraph - Writing incremental jobs reports... INFO 00:16:17,793 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:16:18,152 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB14/SB14.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB14.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:16:18,153 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-50.out INFO 00:18:40,536 QGraph - 6697 Pend, 1 Run, 1 Fail, 48 Done INFO 00:18:40,537 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB14/SB14.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB14.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:18:40,537 QGraph - Writing incremental jobs reports... INFO 00:18:40,537 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:18:40,921 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB15/SB15.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB15.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:18:40,921 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-51.out INFO 00:22:46,317 QGraph - 6696 Pend, 1 Run, 1 Fail, 49 Done INFO 00:22:46,319 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB15/SB15.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB15.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:22:46,319 QGraph - Writing incremental jobs reports... INFO 00:22:46,320 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:22:46,715 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB16/SB16.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB16.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:22:46,715 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-52.out INFO 00:25:21,316 QGraph - 6695 Pend, 1 Run, 1 Fail, 50 Done INFO 00:25:21,318 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB16/SB16.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB16.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:25:21,319 QGraph - Writing incremental jobs reports... INFO 00:25:21,319 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:25:21,673 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB17/SB17.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB17.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:25:21,673 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-53.out INFO 00:28:53,342 QGraph - 6694 Pend, 1 Run, 1 Fail, 51 Done INFO 00:28:53,344 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB17/SB17.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB17.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:28:53,344 QGraph - Writing incremental jobs reports... INFO 00:28:53,345 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:28:53,714 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB18/SB18.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB18.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:28:53,714 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-54.out INFO 00:31:11,031 QGraph - 6693 Pend, 1 Run, 1 Fail, 52 Done INFO 00:31:11,033 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB18/SB18.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB18.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:31:11,033 QGraph - Writing incremental jobs reports... INFO 00:31:11,033 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:31:11,385 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB19/SB19.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB19.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:31:11,385 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-55.out INFO 00:35:59,426 QGraph - 6692 Pend, 1 Run, 1 Fail, 53 Done INFO 00:35:59,428 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB19/SB19.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB19.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:35:59,428 QGraph - Writing incremental jobs reports... INFO 00:35:59,429 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:35:59,801 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB20/SB20.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB20.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:35:59,801 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-56.out INFO 00:39:50,650 QGraph - 6691 Pend, 1 Run, 1 Fail, 54 Done INFO 00:39:50,651 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB20/SB20.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB20.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:39:50,652 QGraph - Writing incremental jobs reports... INFO 00:39:50,652 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:39:51,017 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB21/SB21.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB21.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:39:51,017 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-57.out INFO 00:41:57,517 QGraph - 6690 Pend, 1 Run, 1 Fail, 55 Done INFO 00:41:57,519 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB21/SB21.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB21.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:41:57,519 QGraph - Writing incremental jobs reports... INFO 00:41:57,519 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:41:57,882 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB22/SB22.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB22.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:41:57,882 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-58.out INFO 00:46:05,406 QGraph - 6689 Pend, 1 Run, 1 Fail, 56 Done INFO 00:46:05,408 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB22/SB22.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB22.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:46:05,409 QGraph - Writing incremental jobs reports... INFO 00:46:05,409 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:46:05,804 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB23/SB23.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB23.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:46:05,804 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-59.out INFO 00:48:14,034 QGraph - 6688 Pend, 1 Run, 1 Fail, 57 Done INFO 00:48:14,035 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB23/SB23.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB23.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:48:14,036 QGraph - Writing incremental jobs reports... INFO 00:48:14,036 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:48:14,432 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB24/SB24.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB24.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:48:14,432 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-60.out INFO 00:51:41,664 QGraph - 6687 Pend, 1 Run, 1 Fail, 58 Done INFO 00:51:41,665 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB24/SB24.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB24.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:51:41,666 QGraph - Writing incremental jobs reports... INFO 00:51:41,666 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:51:42,021 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB25/SB25.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB25.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:51:42,021 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-61.out INFO 00:54:17,652 QGraph - 6686 Pend, 1 Run, 1 Fail, 59 Done INFO 00:54:17,654 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB25/SB25.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB25.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:54:17,655 QGraph - Writing incremental jobs reports... INFO 00:54:17,655 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:54:18,016 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB26/SB26.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB26.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:54:18,017 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-62.out INFO 00:56:24,948 QGraph - 6685 Pend, 1 Run, 1 Fail, 60 Done INFO 00:56:24,950 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB26/SB26.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB26.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:56:24,951 QGraph - Writing incremental jobs reports... INFO 00:56:24,951 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:56:25,296 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB27/SB27.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB27.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:56:25,296 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-63.out INFO 00:58:51,143 QGraph - 6684 Pend, 1 Run, 1 Fail, 61 Done INFO 00:58:51,145 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB27/SB27.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB27.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:58:51,145 QGraph - Writing incremental jobs reports... INFO 00:58:51,146 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 00:58:51,489 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB28/SB28.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB28.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 00:58:51,490 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-64.out INFO 01:03:12,381 QGraph - 6683 Pend, 1 Run, 1 Fail, 62 Done INFO 01:03:12,383 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB28/SB28.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB28.realn.depth.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-ploidyMapFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.ploidymap.txt' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-readDepthMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.rdmask.bed' '-minMapQ' '10' '-insertSizeRadius' '10.0' INFO 01:03:12,384 QGraph - Writing incremental jobs reports... INFO 01:03:12,384 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 01:03:12,741 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadDepthCoverage' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB1.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB2.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB3.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB4.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB5.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB6.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB7.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB8.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB9.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB10.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB11.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB12.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB13.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB14.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB15.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB16.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB17.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB18.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB19.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB20.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB21.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB22.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB23.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB24.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB25.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB26.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB27.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB28.realn.depth.txt' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth.dat' INFO 01:03:12,741 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-65.out INFO 01:03:17,477 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB1/SB1.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB1.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:03:17,478 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-66.out INFO 01:11:52,992 QGraph - 6681 Pend, 2 Run, 1 Fail, 63 Done ERROR 01:11:53,002 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadDepthCoverage' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB1.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB2.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB3.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB4.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB5.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB6.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB7.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB8.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB9.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB10.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB11.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB12.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB13.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB14.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB15.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB16.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB17.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB18.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB19.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB20.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB21.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB22.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB23.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB24.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB25.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB26.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB27.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB28.realn.depth.txt' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth.dat' ERROR 01:11:53,003 FunctionEdge - Contents of /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-65.out: INFO 01:03:17,400 HelpFormatter - --------------------------------------------------------------- INFO 01:03:17,403 HelpFormatter - Program Name: org.broadinstitute.sv.apps.MergeReadDepthCoverage INFO 01:03:17,408 HelpFormatter - Program Args: -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB1.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB2.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB3.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB4.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB5.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB6.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB7.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB8.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB9.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB10.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB11.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB12.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB13.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB14.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB15.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB16.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB17.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB18.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB19.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB20.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB21.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB22.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB23.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB24.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB25.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB26.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB27.realn.depth.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB28.realn.depth.txt -O /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth.dat INFO 01:03:17,415 HelpFormatter - Executing as xiayan@localhost.localdomain on Linux 2.6.32-431.3.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_45-mockbuild_2013_11_22_18_30-b00. INFO 01:03:17,415 HelpFormatter - Date/Time: 2015/05/09 01:03:17 INFO 01:03:17,415 HelpFormatter - --------------------------------------------------------------- INFO 01:03:17,416 HelpFormatter - --------------------------------------------------------------- INFO 01:03:17,453 CommandLineProgram - Program completed. INFO 01:11:53,004 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB1/SB1.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB1.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:11:53,004 QGraph - Writing incremental jobs reports... INFO 01:11:53,005 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 01:11:53,356 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB2/SB2.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB2.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:11:53,356 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-67.out INFO 01:23:35,559 QGraph - 6680 Pend, 1 Run, 2 Fail, 64 Done INFO 01:23:35,561 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB2/SB2.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB2.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:23:35,561 QGraph - Writing incremental jobs reports... INFO 01:23:35,562 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 01:23:35,929 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB3/SB3.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB3.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:23:35,930 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-68.out INFO 01:27:21,192 QGraph - 6679 Pend, 1 Run, 2 Fail, 65 Done INFO 01:27:21,194 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB3/SB3.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB3.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:27:21,194 QGraph - Writing incremental jobs reports... INFO 01:27:21,194 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 01:27:21,544 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB4/SB4.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB4.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:27:21,545 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-69.out INFO 01:31:12,698 QGraph - 6678 Pend, 1 Run, 2 Fail, 66 Done INFO 01:31:12,700 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB4/SB4.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB4.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:31:12,701 QGraph - Writing incremental jobs reports... INFO 01:31:12,701 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 01:31:13,134 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB5/SB5.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB5.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:31:13,134 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-70.out INFO 01:41:21,860 QGraph - 6677 Pend, 1 Run, 2 Fail, 67 Done INFO 01:41:21,861 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB5/SB5.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB5.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:41:21,861 QGraph - Writing incremental jobs reports... INFO 01:41:21,861 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 01:41:22,201 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB6/SB6.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB6.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:41:22,202 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-71.out INFO 01:50:56,583 QGraph - 6676 Pend, 1 Run, 2 Fail, 68 Done INFO 01:50:56,585 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB6/SB6.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB6.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:50:56,585 QGraph - Writing incremental jobs reports... INFO 01:50:56,585 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 01:50:56,938 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB7/SB7.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB7.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:50:56,939 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-72.out INFO 01:54:30,872 QGraph - 6675 Pend, 1 Run, 2 Fail, 69 Done INFO 01:54:30,873 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB7/SB7.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB7.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:54:30,873 QGraph - Writing incremental jobs reports... INFO 01:54:30,874 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 01:54:31,231 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB8/SB8.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB8.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:54:31,231 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-73.out INFO 01:58:36,932 QGraph - 6674 Pend, 1 Run, 2 Fail, 70 Done INFO 01:58:36,934 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB8/SB8.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB8.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:58:36,934 QGraph - Writing incremental jobs reports... INFO 01:58:36,935 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 01:58:37,290 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB9/SB9.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB9.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 01:58:37,291 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-74.out INFO 02:02:07,077 QGraph - 6673 Pend, 1 Run, 2 Fail, 71 Done INFO 02:02:07,079 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB9/SB9.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB9.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:02:07,079 QGraph - Writing incremental jobs reports... INFO 02:02:07,080 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:02:07,449 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB10/SB10.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB10.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:02:07,449 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-75.out INFO 02:05:59,511 QGraph - 6672 Pend, 1 Run, 2 Fail, 72 Done INFO 02:05:59,513 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB10/SB10.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB10.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:05:59,513 QGraph - Writing incremental jobs reports... INFO 02:05:59,513 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:05:59,871 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB11/SB11.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB11.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:05:59,871 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-76.out INFO 02:16:22,039 QGraph - 6671 Pend, 1 Run, 2 Fail, 73 Done INFO 02:16:22,041 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB11/SB11.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB11.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:16:22,041 QGraph - Writing incremental jobs reports... INFO 02:16:22,041 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:16:22,410 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB12/SB12.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB12.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:16:22,410 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-77.out INFO 02:19:41,601 QGraph - 6670 Pend, 1 Run, 2 Fail, 74 Done INFO 02:19:41,602 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB12/SB12.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB12.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:19:41,603 QGraph - Writing incremental jobs reports... INFO 02:19:41,603 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:19:41,977 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB13/SB13.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB13.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:19:41,977 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-78.out INFO 02:25:13,802 QGraph - 6669 Pend, 1 Run, 2 Fail, 75 Done INFO 02:25:13,804 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB13/SB13.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB13.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:25:13,804 QGraph - Writing incremental jobs reports... INFO 02:25:13,804 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:25:14,155 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB14/SB14.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB14.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:25:14,155 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-79.out INFO 02:27:47,519 QGraph - 6668 Pend, 1 Run, 2 Fail, 76 Done INFO 02:27:47,521 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB14/SB14.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB14.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:27:47,521 QGraph - Writing incremental jobs reports... INFO 02:27:47,521 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:27:47,884 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB15/SB15.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB15.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:27:47,884 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-80.out INFO 02:32:14,492 QGraph - 6667 Pend, 1 Run, 2 Fail, 77 Done INFO 02:32:14,494 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB15/SB15.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB15.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:32:14,494 QGraph - Writing incremental jobs reports... INFO 02:32:14,495 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:32:14,865 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB16/SB16.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB16.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:32:14,866 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-81.out INFO 02:34:59,854 QGraph - 6666 Pend, 1 Run, 2 Fail, 78 Done INFO 02:34:59,855 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB16/SB16.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB16.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:34:59,856 QGraph - Writing incremental jobs reports... INFO 02:34:59,856 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:35:00,213 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB17/SB17.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB17.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:35:00,213 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-82.out INFO 02:39:19,081 QGraph - 6665 Pend, 1 Run, 2 Fail, 79 Done INFO 02:39:19,082 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB17/SB17.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB17.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:39:19,083 QGraph - Writing incremental jobs reports... INFO 02:39:19,083 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:39:19,445 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB18/SB18.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB18.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:39:19,446 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-83.out INFO 02:41:39,110 QGraph - 6664 Pend, 1 Run, 2 Fail, 80 Done INFO 02:41:39,112 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB18/SB18.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB18.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:41:39,112 QGraph - Writing incremental jobs reports... INFO 02:41:39,113 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:41:39,469 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB19/SB19.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB19.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:41:39,469 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-84.out INFO 02:46:07,978 QGraph - 6663 Pend, 1 Run, 2 Fail, 81 Done INFO 02:46:07,980 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB19/SB19.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB19.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:46:07,980 QGraph - Writing incremental jobs reports... INFO 02:46:07,980 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:46:08,350 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB20/SB20.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB20.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:46:08,350 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-85.out INFO 02:50:47,948 QGraph - 6662 Pend, 1 Run, 2 Fail, 82 Done INFO 02:50:47,950 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB20/SB20.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB20.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:50:47,950 QGraph - Writing incremental jobs reports... INFO 02:50:47,950 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:50:48,303 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB21/SB21.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB21.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:50:48,303 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-86.out INFO 02:52:57,177 QGraph - 6661 Pend, 1 Run, 2 Fail, 83 Done INFO 02:52:57,179 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB21/SB21.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB21.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:52:57,179 QGraph - Writing incremental jobs reports... INFO 02:52:57,179 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:52:57,564 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB22/SB22.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB22.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:52:57,564 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-87.out INFO 02:56:59,952 QGraph - 6660 Pend, 1 Run, 2 Fail, 84 Done INFO 02:56:59,954 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB22/SB22.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB22.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:56:59,954 QGraph - Writing incremental jobs reports... INFO 02:56:59,954 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:57:00,353 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB23/SB23.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB23.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:57:00,354 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-88.out INFO 02:59:22,595 QGraph - 6659 Pend, 1 Run, 2 Fail, 85 Done INFO 02:59:22,597 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB23/SB23.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB23.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:59:22,597 QGraph - Writing incremental jobs reports... INFO 02:59:22,597 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 02:59:22,982 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB24/SB24.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB24.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 02:59:22,983 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-89.out INFO 03:03:13,258 QGraph - 6658 Pend, 1 Run, 2 Fail, 86 Done INFO 03:03:13,260 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB24/SB24.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB24.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 03:03:13,260 QGraph - Writing incremental jobs reports... INFO 03:03:13,260 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:03:13,632 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB25/SB25.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB25.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 03:03:13,632 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-90.out INFO 03:06:23,509 QGraph - 6657 Pend, 1 Run, 2 Fail, 87 Done INFO 03:06:23,511 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB25/SB25.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB25.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 03:06:23,511 QGraph - Writing incremental jobs reports... INFO 03:06:23,511 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:06:23,907 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB26/SB26.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB26.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 03:06:23,907 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-91.out INFO 03:08:36,138 QGraph - 6656 Pend, 1 Run, 2 Fail, 88 Done INFO 03:08:36,139 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB26/SB26.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB26.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 03:08:36,140 QGraph - Writing incremental jobs reports... INFO 03:08:36,140 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:08:36,522 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB27/SB27.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB27.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 03:08:36,522 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-92.out INFO 03:11:08,501 QGraph - 6655 Pend, 1 Run, 2 Fail, 89 Done INFO 03:11:08,503 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB27/SB27.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB27.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 03:11:08,503 QGraph - Writing incremental jobs reports... INFO 03:11:08,504 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:11:08,863 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB28/SB28.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB28.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 03:11:08,863 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-93.out INFO 03:15:28,600 QGraph - 6654 Pend, 1 Run, 2 Fail, 90 Done INFO 03:15:28,602 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB28/SB28.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB28.realn.spans.txt' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-maxInsertSizeStandardDeviations' '3' INFO 03:15:28,603 QGraph - Writing incremental jobs reports... INFO 03:15:28,603 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:15:28,965 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadSpanCoverage' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB1.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB2.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB3.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB4.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB5.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB6.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB7.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB8.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB9.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB10.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB11.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB12.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB13.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB14.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB15.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB16.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB17.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB18.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB19.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB20.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB21.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB22.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB23.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB24.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB25.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB26.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB27.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB28.realn.spans.txt' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans.dat' INFO 03:15:28,965 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-94.out INFO 03:15:35,683 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB1/SB1.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB1.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 03:15:35,683 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-124.out INFO 03:24:20,454 QGraph - 6652 Pend, 2 Run, 2 Fail, 91 Done ERROR 03:24:20,464 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadSpanCoverage' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB1.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB2.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB3.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB4.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB5.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB6.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB7.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB8.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB9.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB10.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB11.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB12.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB13.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB14.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB15.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB16.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB17.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB18.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB19.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB20.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB21.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB22.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB23.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB24.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB25.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB26.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB27.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB28.realn.spans.txt' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans.dat' ERROR 03:24:20,464 FunctionEdge - Contents of /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-94.out: INFO 03:15:35,522 HelpFormatter - -------------------------------------------------------------- INFO 03:15:35,524 HelpFormatter - Program Name: org.broadinstitute.sv.apps.MergeReadSpanCoverage INFO 03:15:35,530 HelpFormatter - Program Args: -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB1.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB2.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB3.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB4.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB5.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB6.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB7.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB8.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB9.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB10.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB11.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB12.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB13.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB14.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB15.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB16.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB17.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB18.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB19.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB20.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB21.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB22.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB23.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB24.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB25.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB26.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB27.realn.spans.txt -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB28.realn.spans.txt -O /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans.dat INFO 03:15:35,536 HelpFormatter - Executing as xiayan@localhost.localdomain on Linux 2.6.32-431.3.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_45-mockbuild_2013_11_22_18_30-b00. INFO 03:15:35,537 HelpFormatter - Date/Time: 2015/05/09 03:15:35 INFO 03:15:35,537 HelpFormatter - -------------------------------------------------------------- INFO 03:15:35,537 HelpFormatter - -------------------------------------------------------------- INFO 03:15:35,602 CommandLineProgram - Program completed. INFO 03:24:20,465 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB1/SB1.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB1.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 03:24:20,465 QGraph - Writing incremental jobs reports... INFO 03:24:20,466 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:24:20,799 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB1.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB1.realn.rc.bin.idx' INFO 03:24:20,799 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-125.out INFO 03:24:52,804 QGraph - 6651 Pend, 1 Run, 3 Fail, 92 Done INFO 03:24:52,806 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB1.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB1.realn.rc.bin.idx' INFO 03:24:52,806 QGraph - Writing incremental jobs reports... INFO 03:24:52,807 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:24:53,165 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB2/SB2.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB2.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 03:24:53,165 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-126.out INFO 03:36:42,497 QGraph - 6650 Pend, 1 Run, 3 Fail, 93 Done INFO 03:36:42,499 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB2/SB2.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB2.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 03:36:42,500 QGraph - Writing incremental jobs reports... INFO 03:36:42,500 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:36:42,866 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB2.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB2.realn.rc.bin.idx' INFO 03:36:42,867 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-127.out INFO 03:37:16,926 QGraph - 6649 Pend, 1 Run, 3 Fail, 94 Done INFO 03:37:16,927 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB2.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB2.realn.rc.bin.idx' INFO 03:37:16,927 QGraph - Writing incremental jobs reports... INFO 03:37:16,928 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:37:17,276 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB3/SB3.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB3.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 03:37:17,276 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-128.out INFO 03:41:48,799 QGraph - 6648 Pend, 1 Run, 3 Fail, 95 Done INFO 03:41:48,801 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB3/SB3.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB3.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 03:41:48,801 QGraph - Writing incremental jobs reports... INFO 03:41:48,802 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:41:49,144 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB3.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB3.realn.rc.bin.idx' INFO 03:41:49,144 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-129.out INFO 03:42:18,451 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB4/SB4.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB4.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 03:42:18,451 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-130.out INFO 03:46:19,552 QGraph - 6646 Pend, 2 Run, 3 Fail, 96 Done INFO 03:46:19,554 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB3.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB3.realn.rc.bin.idx' INFO 03:46:19,555 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB4/SB4.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB4.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 03:46:19,556 QGraph - Writing incremental jobs reports... INFO 03:46:19,556 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:46:19,915 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB4.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB4.realn.rc.bin.idx' INFO 03:46:19,915 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-131.out INFO 03:46:49,721 QGraph - 6645 Pend, 1 Run, 3 Fail, 98 Done INFO 03:46:49,723 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB4.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB4.realn.rc.bin.idx' INFO 03:46:49,723 QGraph - Writing incremental jobs reports... INFO 03:46:49,724 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:46:50,098 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB5/SB5.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB5.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 03:46:50,098 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-132.out INFO 03:57:11,972 QGraph - 6644 Pend, 1 Run, 3 Fail, 99 Done INFO 03:57:11,982 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB5/SB5.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB5.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 03:57:11,983 QGraph - Writing incremental jobs reports... INFO 03:57:11,983 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:57:12,344 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB5.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB5.realn.rc.bin.idx' INFO 03:57:12,345 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-133.out INFO 03:57:45,380 QGraph - 6643 Pend, 1 Run, 3 Fail, 100 Done INFO 03:57:45,381 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB5.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB5.realn.rc.bin.idx' INFO 03:57:45,382 QGraph - Writing incremental jobs reports... INFO 03:57:45,382 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 03:57:45,724 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB6/SB6.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB6.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 03:57:45,724 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-134.out INFO 04:07:06,116 QGraph - 6642 Pend, 1 Run, 3 Fail, 101 Done INFO 04:07:06,118 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB6/SB6.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB6.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:07:06,119 QGraph - Writing incremental jobs reports... INFO 04:07:06,119 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:07:06,487 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB6.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB6.realn.rc.bin.idx' INFO 04:07:06,487 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-135.out INFO 04:07:39,194 QGraph - 6641 Pend, 1 Run, 3 Fail, 102 Done INFO 04:07:39,196 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB6.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB6.realn.rc.bin.idx' INFO 04:07:39,196 QGraph - Writing incremental jobs reports... INFO 04:07:39,196 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:07:39,551 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB7/SB7.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB7.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:07:39,551 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-136.out INFO 04:11:27,842 QGraph - 6640 Pend, 1 Run, 3 Fail, 103 Done INFO 04:11:27,843 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB7/SB7.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB7.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:11:27,844 QGraph - Writing incremental jobs reports... INFO 04:11:27,844 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:11:28,211 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB7.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB7.realn.rc.bin.idx' INFO 04:11:28,211 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-137.out INFO 04:11:57,689 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB8/SB8.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB8.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:11:57,690 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-138.out INFO 04:16:23,727 QGraph - 6638 Pend, 2 Run, 3 Fail, 104 Done INFO 04:16:23,729 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB7.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB7.realn.rc.bin.idx' INFO 04:16:23,730 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB8/SB8.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB8.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:16:23,731 QGraph - Writing incremental jobs reports... INFO 04:16:23,731 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:16:24,089 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB8.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB8.realn.rc.bin.idx' INFO 04:16:24,089 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-139.out INFO 04:16:54,007 QGraph - 6637 Pend, 1 Run, 3 Fail, 106 Done INFO 04:16:54,008 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB8.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB8.realn.rc.bin.idx' INFO 04:16:54,009 QGraph - Writing incremental jobs reports... INFO 04:16:54,009 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:16:54,369 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB9/SB9.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB9.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:16:54,369 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-140.out INFO 04:20:44,472 QGraph - 6636 Pend, 1 Run, 3 Fail, 107 Done INFO 04:20:44,474 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB9/SB9.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB9.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:20:44,474 QGraph - Writing incremental jobs reports... INFO 04:20:44,475 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:20:44,821 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB9.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB9.realn.rc.bin.idx' INFO 04:20:44,821 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-141.out INFO 04:21:14,084 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB10/SB10.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB10.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:21:14,085 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-142.out INFO 04:25:23,742 QGraph - 6634 Pend, 2 Run, 3 Fail, 108 Done INFO 04:25:23,744 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB9.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB9.realn.rc.bin.idx' INFO 04:25:23,745 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB10/SB10.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB10.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:25:23,745 QGraph - Writing incremental jobs reports... INFO 04:25:23,746 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:25:24,107 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB10.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB10.realn.rc.bin.idx' INFO 04:25:24,108 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-143.out INFO 04:25:53,706 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB11/SB11.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB11.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:25:53,706 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-144.out INFO 04:36:18,415 QGraph - 6632 Pend, 2 Run, 3 Fail, 110 Done ERROR 04:36:18,417 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB10.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB10.realn.rc.bin.idx' ERROR 04:36:18,418 FunctionEdge - Contents of /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-143.out: INFO 04:25:28,807 HelpFormatter - ----------------------------------------------------------- INFO 04:25:28,810 HelpFormatter - Program Name: org.broadinstitute.sv.apps.IndexReadCountFile INFO 04:25:28,816 HelpFormatter - Program Args: -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB10.realn.rc.bin -O /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB10.realn.rc.bin.idx INFO 04:25:28,823 HelpFormatter - Executing as xiayan@localhost.localdomain on Linux 2.6.32-431.3.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_45-mockbuild_2013_11_22_18_30-b00. INFO 04:25:28,823 HelpFormatter - Date/Time: 2015/05/09 04:25:28 INFO 04:25:28,824 HelpFormatter - ----------------------------------------------------------- INFO 04:25:28,824 HelpFormatter - ----------------------------------------------------------- INFO 04:25:53,692 CommandLineProgram - Program completed. INFO 04:36:18,419 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB11/SB11.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB11.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:36:18,419 QGraph - Writing incremental jobs reports... INFO 04:36:18,420 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:36:18,768 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB11.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB11.realn.rc.bin.idx' INFO 04:36:18,768 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-145.out INFO 04:36:52,384 QGraph - 6631 Pend, 1 Run, 4 Fail, 111 Done INFO 04:36:52,387 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB11.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB11.realn.rc.bin.idx' INFO 04:36:52,388 QGraph - Writing incremental jobs reports... INFO 04:36:52,388 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:36:52,711 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB12/SB12.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB12.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:36:52,711 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-146.out INFO 04:40:22,384 QGraph - 6630 Pend, 1 Run, 4 Fail, 112 Done INFO 04:40:22,386 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB12/SB12.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB12.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:40:22,386 QGraph - Writing incremental jobs reports... INFO 04:40:22,386 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:40:22,753 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB12.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB12.realn.rc.bin.idx' INFO 04:40:22,753 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-147.out INFO 04:40:51,871 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB13/SB13.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB13.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:40:51,871 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-148.out INFO 04:46:27,380 QGraph - 6628 Pend, 2 Run, 4 Fail, 113 Done ERROR 04:46:27,382 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB12.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB12.realn.rc.bin.idx' ERROR 04:46:27,383 FunctionEdge - Contents of /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-147.out: INFO 04:40:27,379 HelpFormatter - ----------------------------------------------------------- INFO 04:40:27,382 HelpFormatter - Program Name: org.broadinstitute.sv.apps.IndexReadCountFile INFO 04:40:27,388 HelpFormatter - Program Args: -I /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB12.realn.rc.bin -O /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB12.realn.rc.bin.idx INFO 04:40:27,395 HelpFormatter - Executing as xiayan@localhost.localdomain on Linux 2.6.32-431.3.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_45-mockbuild_2013_11_22_18_30-b00. INFO 04:40:27,395 HelpFormatter - Date/Time: 2015/05/09 04:40:27 INFO 04:40:27,396 HelpFormatter - ----------------------------------------------------------- INFO 04:40:27,396 HelpFormatter - ----------------------------------------------------------- INFO 04:40:51,861 CommandLineProgram - Program completed. INFO 04:46:27,384 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB13/SB13.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB13.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:46:27,384 QGraph - Writing incremental jobs reports... INFO 04:46:27,385 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:46:27,737 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB13.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB13.realn.rc.bin.idx' INFO 04:46:27,737 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-149.out INFO 04:47:00,618 QGraph - 6627 Pend, 1 Run, 5 Fail, 114 Done INFO 04:47:00,619 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB13.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB13.realn.rc.bin.idx' INFO 04:47:00,620 QGraph - Writing incremental jobs reports... INFO 04:47:00,620 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:47:00,976 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB14/SB14.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB14.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:47:00,976 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-150.out INFO 04:49:51,420 QGraph - 6626 Pend, 1 Run, 5 Fail, 115 Done INFO 04:49:51,422 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB14/SB14.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB14.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:49:51,422 QGraph - Writing incremental jobs reports... INFO 04:49:51,422 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:49:51,792 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB14.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB14.realn.rc.bin.idx' INFO 04:49:51,792 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-151.out INFO 04:50:23,407 QGraph - 6625 Pend, 1 Run, 5 Fail, 116 Done INFO 04:50:23,408 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB14.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB14.realn.rc.bin.idx' INFO 04:50:23,408 QGraph - Writing incremental jobs reports... INFO 04:50:23,409 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:50:23,775 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB15/SB15.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB15.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:50:23,775 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-152.out INFO 04:55:03,177 QGraph - 6624 Pend, 1 Run, 5 Fail, 117 Done INFO 04:55:03,179 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB15/SB15.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB15.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:55:03,179 QGraph - Writing incremental jobs reports... INFO 04:55:03,179 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:55:03,540 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB15.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB15.realn.rc.bin.idx' INFO 04:55:03,540 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-153.out INFO 04:55:35,456 QGraph - 6623 Pend, 1 Run, 5 Fail, 118 Done INFO 04:55:35,458 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB15.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB15.realn.rc.bin.idx' INFO 04:55:35,458 QGraph - Writing incremental jobs reports... INFO 04:55:35,458 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:55:35,809 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB16/SB16.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB16.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:55:35,809 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-154.out INFO 04:58:07,009 QGraph - 6622 Pend, 1 Run, 5 Fail, 119 Done INFO 04:58:07,010 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB16/SB16.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB16.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:58:07,011 QGraph - Writing incremental jobs reports... INFO 04:58:07,011 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:58:07,385 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB16.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB16.realn.rc.bin.idx' INFO 04:58:07,385 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-155.out INFO 04:58:37,993 QGraph - 6621 Pend, 1 Run, 5 Fail, 120 Done INFO 04:58:37,995 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB16.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB16.realn.rc.bin.idx' INFO 04:58:37,995 QGraph - Writing incremental jobs reports... INFO 04:58:37,996 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 04:58:38,366 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB17/SB17.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB17.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 04:58:38,366 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-156.out INFO 05:02:43,389 QGraph - 6620 Pend, 1 Run, 5 Fail, 121 Done INFO 05:02:43,391 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB17/SB17.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB17.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:02:43,391 QGraph - Writing incremental jobs reports... INFO 05:02:43,392 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:02:43,758 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB17.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB17.realn.rc.bin.idx' INFO 05:02:43,758 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-157.out INFO 05:03:15,133 QGraph - 6619 Pend, 1 Run, 5 Fail, 122 Done INFO 05:03:15,135 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB17.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB17.realn.rc.bin.idx' INFO 05:03:15,135 QGraph - Writing incremental jobs reports... INFO 05:03:15,136 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:03:15,500 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB18/SB18.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB18.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:03:15,500 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-158.out INFO 05:06:00,249 QGraph - 6618 Pend, 1 Run, 5 Fail, 123 Done INFO 05:06:00,251 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB18/SB18.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB18.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:06:00,251 QGraph - Writing incremental jobs reports... INFO 05:06:00,252 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:06:00,616 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB18.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB18.realn.rc.bin.idx' INFO 05:06:00,616 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-159.out INFO 05:06:31,387 QGraph - 6617 Pend, 1 Run, 5 Fail, 124 Done INFO 05:06:31,389 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB18.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB18.realn.rc.bin.idx' INFO 05:06:31,389 QGraph - Writing incremental jobs reports... INFO 05:06:31,390 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:06:31,738 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB19/SB19.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB19.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:06:31,738 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-160.out INFO 05:11:39,704 QGraph - 6616 Pend, 1 Run, 5 Fail, 125 Done INFO 05:11:39,706 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB19/SB19.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB19.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:11:39,706 QGraph - Writing incremental jobs reports... INFO 05:11:39,706 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:11:40,063 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB19.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB19.realn.rc.bin.idx' INFO 05:11:40,063 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-161.out INFO 05:12:10,835 QGraph - 6615 Pend, 1 Run, 5 Fail, 126 Done INFO 05:12:10,836 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB19.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB19.realn.rc.bin.idx' INFO 05:12:10,837 QGraph - Writing incremental jobs reports... INFO 05:12:10,837 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:12:11,166 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB20/SB20.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB20.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:12:11,166 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-162.out INFO 05:17:00,138 QGraph - 6614 Pend, 1 Run, 5 Fail, 127 Done INFO 05:17:00,139 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB20/SB20.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB20.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:17:00,140 QGraph - Writing incremental jobs reports... INFO 05:17:00,140 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:17:00,509 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB20.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB20.realn.rc.bin.idx' INFO 05:17:00,509 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-163.out INFO 05:17:32,531 QGraph - 6613 Pend, 1 Run, 5 Fail, 128 Done INFO 05:17:32,533 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB20.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB20.realn.rc.bin.idx' INFO 05:17:32,533 QGraph - Writing incremental jobs reports... INFO 05:17:32,533 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:17:32,891 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB21/SB21.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB21.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:17:32,891 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-164.out INFO 05:20:06,338 QGraph - 6612 Pend, 1 Run, 5 Fail, 129 Done INFO 05:20:06,340 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB21/SB21.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB21.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:20:06,340 QGraph - Writing incremental jobs reports... INFO 05:20:06,341 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:20:06,707 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB21.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB21.realn.rc.bin.idx' INFO 05:20:06,707 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-165.out INFO 05:20:37,946 QGraph - 6611 Pend, 1 Run, 5 Fail, 130 Done INFO 05:20:37,948 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB21.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB21.realn.rc.bin.idx' INFO 05:20:37,948 QGraph - Writing incremental jobs reports... INFO 05:20:37,948 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:20:38,318 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB22/SB22.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB22.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:20:38,318 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-166.out INFO 05:24:48,672 QGraph - 6610 Pend, 1 Run, 5 Fail, 131 Done INFO 05:24:48,674 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB22/SB22.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB22.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:24:48,674 QGraph - Writing incremental jobs reports... INFO 05:24:48,674 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:24:49,045 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB22.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB22.realn.rc.bin.idx' INFO 05:24:49,045 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-167.out INFO 05:25:20,478 QGraph - 6609 Pend, 1 Run, 5 Fail, 132 Done INFO 05:25:20,479 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB22.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB22.realn.rc.bin.idx' INFO 05:25:20,480 QGraph - Writing incremental jobs reports... INFO 05:25:20,480 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:25:20,826 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB23/SB23.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB23.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:25:20,826 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-168.out INFO 05:28:01,084 QGraph - 6608 Pend, 1 Run, 5 Fail, 133 Done INFO 05:28:01,085 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB23/SB23.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB23.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:28:01,085 QGraph - Writing incremental jobs reports... INFO 05:28:01,086 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:28:01,438 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB23.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB23.realn.rc.bin.idx' INFO 05:28:01,438 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-169.out INFO 05:28:31,835 QGraph - 6607 Pend, 1 Run, 5 Fail, 134 Done INFO 05:28:31,837 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB23.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB23.realn.rc.bin.idx' INFO 05:28:31,837 QGraph - Writing incremental jobs reports... INFO 05:28:31,838 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:28:32,189 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB24/SB24.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB24.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:28:32,189 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-170.out INFO 05:32:31,731 QGraph - 6606 Pend, 1 Run, 5 Fail, 135 Done INFO 05:32:31,733 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB24/SB24.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB24.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:32:31,734 QGraph - Writing incremental jobs reports... INFO 05:32:31,734 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:32:32,103 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB24.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB24.realn.rc.bin.idx' INFO 05:32:32,103 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-171.out INFO 05:33:03,867 QGraph - 6605 Pend, 1 Run, 5 Fail, 136 Done INFO 05:33:03,869 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB24.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB24.realn.rc.bin.idx' INFO 05:33:03,869 QGraph - Writing incremental jobs reports... INFO 05:33:03,869 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:33:04,198 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB25/SB25.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB25.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:33:04,198 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-172.out INFO 05:36:11,198 QGraph - 6604 Pend, 1 Run, 5 Fail, 137 Done INFO 05:36:11,200 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB25/SB25.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB25.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:36:11,200 QGraph - Writing incremental jobs reports... INFO 05:36:11,201 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:36:11,574 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB25.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB25.realn.rc.bin.idx' INFO 05:36:11,574 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-173.out INFO 05:36:42,648 QGraph - 6603 Pend, 1 Run, 5 Fail, 138 Done INFO 05:36:42,650 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB25.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB25.realn.rc.bin.idx' INFO 05:36:42,650 QGraph - Writing incremental jobs reports... INFO 05:36:42,650 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:36:43,005 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB26/SB26.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB26.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:36:43,005 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-174.out INFO 05:39:38,357 QGraph - 6602 Pend, 1 Run, 5 Fail, 139 Done INFO 05:39:38,358 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB26/SB26.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB26.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:39:38,359 QGraph - Writing incremental jobs reports... INFO 05:39:38,359 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:39:38,732 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB26.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB26.realn.rc.bin.idx' INFO 05:39:38,732 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-175.out INFO 05:40:10,016 QGraph - 6601 Pend, 1 Run, 5 Fail, 140 Done INFO 05:40:10,017 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB26.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB26.realn.rc.bin.idx' INFO 05:40:10,017 QGraph - Writing incremental jobs reports... INFO 05:40:10,018 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:40:10,380 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB27/SB27.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB27.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:40:10,380 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-176.out INFO 05:43:32,057 QGraph - 6600 Pend, 1 Run, 5 Fail, 141 Done INFO 05:43:32,058 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB27/SB27.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB27.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:43:32,059 QGraph - Writing incremental jobs reports... INFO 05:43:32,059 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:43:32,422 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB27.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB27.realn.rc.bin.idx' INFO 05:43:32,422 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-177.out INFO 05:44:02,850 QGraph - 6599 Pend, 1 Run, 5 Fail, 142 Done INFO 05:44:02,852 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB27.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB27.realn.rc.bin.idx' INFO 05:44:02,852 QGraph - Writing incremental jobs reports... INFO 05:44:02,853 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:44:03,200 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB28/SB28.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB28.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:44:03,200 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-178.out INFO 05:48:34,602 QGraph - 6598 Pend, 1 Run, 5 Fail, 143 Done INFO 05:48:34,604 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadCountsWalker' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-I' '/disk/disk1/work/xiayan/data/sequence_ibcas/result/SB28/SB28.realn.bam' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB28.realn.rc.bin' '-disableGATKTraversal' 'true' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-insertSizeRadius' '10.0' INFO 05:48:34,604 QGraph - Writing incremental jobs reports... INFO 05:48:34,604 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:48:34,959 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB28.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB28.realn.rc.bin.idx' INFO 05:48:34,959 FunctionEdge - Output written to /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-179.out INFO 05:49:05,906 QGraph - 6597 Pend, 1 Run, 5 Fail, 144 Done INFO 05:49:05,908 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB28.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB28.realn.rc.bin.idx' INFO 05:49:05,908 QGraph - Writing incremental jobs reports... INFO 05:49:05,908 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:49:06,282 QGraph - 6597 Pend, 0 Run, 5 Fail, 145 Done INFO 05:49:06,290 QCommandLine - Writing final jobs report... INFO 05:49:06,290 QJobsReporter - Writing JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.txt INFO 05:49:06,314 QJobsReporter - Plotting JobLogging GATKReport to file /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SVPreprocess.jobreport.pdf WARN 05:49:10,159 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info. INFO 05:49:10,162 QCommandLine - Done with errors INFO 05:49:10,555 QGraph - ------- INFO 05:49:10,556 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadDepthCoverage' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB1.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB2.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB3.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB4.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB5.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB6.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB7.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB8.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB9.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB10.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB11.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB12.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB13.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB14.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB15.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB16.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB17.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB18.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB19.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB20.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB21.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB22.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB23.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB24.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB25.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB26.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB27.realn.depth.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth/SB28.realn.depth.txt' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/depth.dat' INFO 05:49:10,556 QGraph - Log: /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-65.out INFO 05:49:10,556 QGraph - ------- INFO 05:49:10,557 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadSpanCoverage' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB1.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB2.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB3.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB4.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB5.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB6.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB7.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB8.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB9.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB10.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB11.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB12.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB13.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB14.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB15.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB16.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB17.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB18.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB19.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB20.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB21.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB22.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB23.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB24.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB25.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB26.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB27.realn.spans.txt' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans/SB28.realn.spans.txt' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/spans.dat' INFO 05:49:10,557 QGraph - Log: /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-94.out INFO 05:49:10,557 QGraph - ------- INFO 05:49:10,557 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB10.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB10.realn.rc.bin.idx' INFO 05:49:10,557 QGraph - Log: /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-143.out INFO 05:49:10,557 QGraph - ------- INFO 05:49:10,558 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB12.realn.rc.bin' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/rccache/SB12.realn.rc.bin.idx' INFO 05:49:10,558 QGraph - Log: /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-147.out INFO 05:49:10,558 QGraph - ------- INFO 05:49:10,558 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/SV_TMPDIR' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' '-cp' '/disk/disk1/work/xiayan/bin/svtoolkit/lib/SVToolkit.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/disk/disk1/work/xiayan/bin/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata/gcprofile/reference.gcprof.zip' '-R' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.fasta' '-md' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/metadata' '-writeReferenceProfile' 'true' '-genomeMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.svmask.fasta' '-copyNumberMaskFile' '/disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/data/Sbicolor_v2.1_255_cop.gcmask.fasta' '-configFile' '/disk/disk1/work/xiayan/bin/svtoolkit/conf/genstrip_parameters.txt' INFO 05:49:10,558 QGraph - Log: /disk/disk1/work/xiayan/bin/svtoolkit/sorghum_data/run1/logs/SVPreprocess-5.out INFO 05:49:10,559 QCommandLine - Script failed: 6597 Pend, 0 Run, 5 Fail, 145 Done