load java/1.7.0u25 (PATH, LD_LIBRARY_PATH) load R/2.14.2 (PATH, MANPATH, LD_LIBRARY_PATH) SAMTOOLS/1.0(25):ERROR:150: Module 'SAMTOOLS/1.0' conflicts with the currently loaded module(s) 'SAMTOOLS/1.2' SAMTOOLS/1.0(25):ERROR:102: Tcl command execution failed: conflict $PROG_NAME INFO 21:03:37,454 QScriptManager - Compiling 2 QScripts INFO 21:04:10,508 QScriptManager - Compilation complete INFO 21:04:10,874 HelpFormatter - ---------------------------------------------------------------------- INFO 21:04:10,874 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/01/25 20:42:54 INFO 21:04:10,875 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 21:04:10,875 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 21:04:10,875 HelpFormatter - Program Args: -S /project/devel/mramia/svtoolkit2/qscript/SVPreprocess.q -S /project/devel/mramia/svtoolkit2/qscript/SVQScript.q -gatk /project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar -cp /project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar -tempDir ./tmpdir -configFile genstrip_parameters.txt -R /project/devel/mramia/hg18/hg18.fa -ploidyMapFile /project/devel/mramia/hg18/hg18.ploidymap.txt -genomeMaskFile /project/devel/mramia/hg18/hg18.fa.svmask.fasta -runDirectory test1 -md test1/metadata -reduceInsertSizeDistributions true -computeGCProfiles true -computeReadCounts true -jobLogDir test1/logs -I /project/devel/mramia/french_genome/hg18_sams/bams/French_1and2_merged.bam -run INFO 21:04:10,876 HelpFormatter - Executing as mramia@cn59 on Linux 2.6.32-220.23.1.bl6.Bull.28.8.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15. INFO 21:04:10,876 HelpFormatter - Date/Time: 2015/02/17 21:04:10 INFO 21:04:10,876 HelpFormatter - ---------------------------------------------------------------------- INFO 21:04:10,876 HelpFormatter - ---------------------------------------------------------------------- INFO 21:04:10,883 QCommandLine - Scripting SVPreprocess INFO 21:04:13,164 QCommandLine - Added 806 functions INFO 21:04:13,164 QGraph - Generating graph. INFO 21:04:13,514 QGraph - Running jobs. INFO 21:04:14,317 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateMetaDataDirectory' -l DEBUG '-md' 'test1/metadata' INFO 21:04:14,317 FunctionEdge - Output written to /project/devel/mramia/svtoolkit2/french_genome/test1/logs/SVPreprocess-1.out INFO 21:04:21,176 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/genome_sizes.txt' '-R' '/project/devel/mramia/hg18/hg18.fa' '-ploidyMapFile' '/project/devel/mramia/hg18/hg18.ploidymap.txt' '-genomeMaskFile' '/project/devel/mramia/hg18/hg18.fa.svmask.fasta' INFO 21:04:21,176 FunctionEdge - Output written to /project/devel/mramia/svtoolkit2/french_genome/test1/logs/SVPreprocess-2.out INFO 21:04:28,115 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/project/devel/mramia/hg18/hg18.fa' '-I' '/project/devel/mramia/french_genome/hg18_sams/bams/French_1and2_merged.bam' '-O' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd/French_1and2_merged.hist.bin' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' -createEmpty INFO 21:04:28,115 FunctionEdge - Output written to /project/devel/mramia/svtoolkit2/french_genome/test1/logs/SVPreprocess-4.out INFO 22:44:49,643 QGraph - 803 Pend, 3 Run, 0 Fail, 0 Done ERROR 22:44:49,653 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateMetaDataDirectory' -l DEBUG '-md' 'test1/metadata' ERROR 22:44:49,657 FunctionEdge - Contents of /project/devel/mramia/svtoolkit2/french_genome/test1/logs/SVPreprocess-1.out: INFO 21:04:21,123 HelpFormatter - ---------------------------------------------------------------- INFO 21:04:21,129 HelpFormatter - Program Name: org.broadinstitute.sv.apps.CreateMetaDataDirectory DEBUG 21:04:21,131 HelpFormatter - Current directory: /project/devel/mramia/svtoolkit2/french_genome INFO 21:04:21,136 HelpFormatter - Program Args: -l DEBUG -md test1/metadata INFO 21:04:21,139 HelpFormatter - Executing as mramia@cn59 on Linux 2.6.32-220.23.1.bl6.Bull.28.8.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15. INFO 21:04:21,140 HelpFormatter - Date/Time: 2015/02/17 21:04:21 INFO 21:04:21,140 HelpFormatter - ---------------------------------------------------------------- INFO 21:04:21,140 HelpFormatter - ---------------------------------------------------------------- INFO 21:04:21,142 MetaData - Opening metadata ... INFO 21:04:21,143 MetaData - Adding metadata directory test1/metadata ... INFO 21:04:21,144 MetaData - Opened metadata. INFO 21:04:21,147 CommandLineProgram - Program completed. ERROR 22:44:49,663 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/genome_sizes.txt' '-R' '/project/devel/mramia/hg18/hg18.fa' '-ploidyMapFile' '/project/devel/mramia/hg18/hg18.ploidymap.txt' '-genomeMaskFile' '/project/devel/mramia/hg18/hg18.fa.svmask.fasta' ERROR 22:44:49,675 FunctionEdge - Contents of /project/devel/mramia/svtoolkit2/french_genome/test1/logs/SVPreprocess-2.out: INFO 21:04:27,993 HelpFormatter - ----------------------------------------------------------- INFO 21:04:27,999 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ComputeGenomeSizes INFO 21:04:28,004 HelpFormatter - Program Args: -O /project/devel/mramia/svtoolkit2/french_genome/test1/metadata/genome_sizes.txt -R /project/devel/mramia/hg18/hg18.fa -ploidyMapFile /project/devel/mramia/hg18/hg18.ploidymap.txt -genomeMaskFile /project/devel/mramia/hg18/hg18.fa.svmask.fasta INFO 21:04:28,006 HelpFormatter - Executing as mramia@cn59 on Linux 2.6.32-220.23.1.bl6.Bull.28.8.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15. INFO 21:04:28,007 HelpFormatter - Date/Time: 2015/02/17 21:04:27 INFO 21:04:28,007 HelpFormatter - ----------------------------------------------------------- INFO 21:04:28,007 HelpFormatter - ----------------------------------------------------------- INFO 21:04:28,056 ComputeGenomeSizes - Processing interval chr10:1-135374737 ... Exception in thread "main" org.broadinstitute.sv.commandline.ArgumentException: Mismatch found between genome mask and reference sequence: Interval chr10:1-135374737 not found in genome mask at org.broadinstitute.sv.apps.ComputeGenomeSizes.run(ComputeGenomeSizes.java:76) at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:50) 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.ComputeGenomeSizes.main(ComputeGenomeSizes.java:57) INFO 22:44:49,682 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '/project/devel/mramia/hg18/hg18.fa' '-I' '/project/devel/mramia/french_genome/hg18_sams/bams/French_1and2_merged.bam' '-O' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd/French_1and2_merged.hist.bin' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' -createEmpty INFO 22:44:49,683 QGraph - Writing incremental jobs reports... INFO 22:44:49,690 QJobsReporter - Writing JobLogging GATKReport to file /project/devel/mramia/svtoolkit2/french_genome/SVPreprocess.jobreport.txt INFO 22:44:49,775 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeInsertSizeHistograms' '-I' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd/French_1and2_merged.hist.bin' '-O' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd.hist.bin' INFO 22:44:49,775 FunctionEdge - Output written to /project/devel/mramia/svtoolkit2/french_genome/test1/logs/SVPreprocess-5.out INFO 22:44:56,987 QGraph - 802 Pend, 1 Run, 2 Fail, 1 Done INFO 22:45:19,657 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeInsertSizeHistograms' '-I' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd/French_1and2_merged.hist.bin' '-O' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd.hist.bin' INFO 22:45:19,658 QGraph - Writing incremental jobs reports... INFO 22:45:19,658 QJobsReporter - Writing JobLogging GATKReport to file /project/devel/mramia/svtoolkit2/french_genome/SVPreprocess.jobreport.txt INFO 22:45:19,732 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd.hist.bin' '-O' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd.dist.bin' INFO 22:45:19,732 FunctionEdge - Output written to /project/devel/mramia/svtoolkit2/french_genome/test1/logs/SVPreprocess-6.out INFO 22:45:26,664 QGraph - 801 Pend, 1 Run, 2 Fail, 2 Done INFO 22:45:49,666 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd.hist.bin' '-O' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd.dist.bin' INFO 22:45:49,666 QGraph - Writing incremental jobs reports... INFO 22:45:49,667 QJobsReporter - Writing JobLogging GATKReport to file /project/devel/mramia/svtoolkit2/french_genome/SVPreprocess.jobreport.txt INFO 22:45:49,727 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeInsertStatistics' '-I' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd.dist.bin' '-O' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd.stats.dat' INFO 22:45:49,727 FunctionEdge - Output written to /project/devel/mramia/svtoolkit2/french_genome/test1/logs/SVPreprocess-7.out INFO 22:45:56,621 QGraph - 800 Pend, 1 Run, 2 Fail, 3 Done INFO 22:46:19,666 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeInsertStatistics' '-I' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd.dist.bin' '-O' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/isd.stats.dat' INFO 22:46:19,667 QGraph - Writing incremental jobs reports... INFO 22:46:19,667 QJobsReporter - Writing JobLogging GATKReport to file /project/devel/mramia/svtoolkit2/french_genome/SVPreprocess.jobreport.txt INFO 22:46:19,705 QGraph - 800 Pend, 0 Run, 2 Fail, 4 Done INFO 22:46:19,718 QCommandLine - Writing final jobs report... INFO 22:46:19,718 QJobsReporter - Writing JobLogging GATKReport to file /project/devel/mramia/svtoolkit2/french_genome/SVPreprocess.jobreport.txt INFO 22:46:19,773 QJobsReporter - Plotting JobLogging GATKReport to file /project/devel/mramia/svtoolkit2/french_genome/SVPreprocess.jobreport.pdf WARN 22:46:21,065 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info. INFO 22:46:21,066 QCommandLine - Done with errors INFO 22:46:21,178 QGraph - ------- INFO 22:46:21,179 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateMetaDataDirectory' -l DEBUG '-md' 'test1/metadata' INFO 22:46:21,179 QGraph - Log: /project/devel/mramia/svtoolkit2/french_genome/test1/logs/SVPreprocess-1.out INFO 22:46:21,180 QGraph - ------- INFO 22:46:21,181 QGraph - Failed: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/project/devel/mramia/svtoolkit2/french_genome/tmpdir' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' '-cp' '/project/devel/mramia/svtoolkit2/lib/SVToolkit.jar:/project/devel/mramia/svtoolkit2/lib/gatk/GenomeAnalysisTK.jar:/project/devel/mramia/svtoolkit2/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O' '/project/devel/mramia/svtoolkit2/french_genome/test1/metadata/genome_sizes.txt' '-R' '/project/devel/mramia/hg18/hg18.fa' '-ploidyMapFile' '/project/devel/mramia/hg18/hg18.ploidymap.txt' '-genomeMaskFile' '/project/devel/mramia/hg18/hg18.fa.svmask.fasta' INFO 22:46:21,181 QGraph - Log: /project/devel/mramia/svtoolkit2/french_genome/test1/logs/SVPreprocess-2.out INFO 22:46:21,202 QCommandLine - Script failed: 800 Pend, 0 Run, 2 Fail, 4 Done real 103m3.450s user 42m49.960s sys 58m38.170s