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SVToolkit version 1.04 (build 1456)
Build date: 2014/09/22 13:56:33
Web site: http://www.broadinstitute.org/software/genomestrip
INFO 11:14:19,448 QScriptManager - Compiling 2 QScripts
INFO 11:14:52,656 QScriptManager - Compilation complete
INFO 11:14:53,229 HelpFormatter - ----------------------------------------------------------------------
INFO 11:14:53,229 HelpFormatter - Queue v2.5-2-g5671483, Compiled 2013/08/22 15:09:27
INFO 11:14:53,230 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO 11:14:53,230 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:14:53,230 HelpFormatter - Program Args: -S ~/svtoolkit/qscript/SVPreprocess.q -S ~/svtoolkit/qscript/SVQScript.q -gatk ~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar --disableJobReport -cp ~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -ploidyMapFile data/human_b36_chr1.ploidy.map -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -disableGATKTraversal -useMultiStep -computeMetadataOverInterval 1:61699966-61900017 -computeGCProfiles -jobLogDir test1/logs -I data/installtest.bam -run
INFO 11:14:53,230 HelpFormatter - Date/Time: 2015/01/26 11:14:53
INFO 11:14:53,231 HelpFormatter - ----------------------------------------------------------------------
INFO 11:14:53,231 HelpFormatter - ----------------------------------------------------------------------
INFO 11:14:53,238 QCommandLine - Scripting SVPreprocess
INFO 11:14:53,539 QCommandLine - Added 12 functions
INFO 11:14:53,539 QGraph - Generating graph.
INFO 11:14:53,560 QGraph - Running jobs.
INFO 11:14:53,602 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateMetaDataDirectory' -l DEBUG '-md' 'test1/metadata'
INFO 11:14:53,603 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVPreprocess-1.out
INFO 11:15:02,967 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O' '~/svtoolkit/installtest/test1/metadata/genome_sizes.txt' '-R' 'data/human_b36_chr1.fasta' '-ploidyMapFile' 'data/human_b36_chr1.ploidy.map' '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' '-genomeInterval' '1:61699966-61900017'
INFO 11:15:02,967 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVPreprocess-2.out
INFO 11:15:13,889 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '~/svtoolkit/installtest/data/human_b36_chr1.fasta' '-I' 'data/installtest.bam' '-O' '~/svtoolkit/installtest/test1/metadata/isd/installtest.hist.bin' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' -createEmpty
INFO 11:15:13,889 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVPreprocess-4.out
INFO 11:15:27,843 QGraph - 9 Pend, 3 Run, 0 Fail, 0 Done
INFO 11:15:27,852 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.CreateMetaDataDirectory' -l DEBUG '-md' 'test1/metadata'
INFO 11:15:27,859 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O' '~/svtoolkit/installtest/test1/metadata/genome_sizes.txt' '-R' 'data/human_b36_chr1.fasta' '-ploidyMapFile' 'data/human_b36_chr1.ploidy.map' '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' '-genomeInterval' '1:61699966-61900017'
INFO 11:15:27,865 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeInsertSizeHistogramsWalker' '-R' '~/svtoolkit/installtest/data/human_b36_chr1.fasta' '-I' 'data/installtest.bam' '-O' '~/svtoolkit/installtest/test1/metadata/isd/installtest.hist.bin' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' -createEmpty
INFO 11:15:27,865 QGraph - Writing incremental jobs reports...
INFO 11:15:27,868 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' '~/svtoolkit/installtest/test1/metadata/gcprofile/reference.gcprof.zip' '-R' 'data/human_b36_chr1.fasta' '-md' 'test1/metadata' '-writeReferenceProfile' 'true' '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' '-copyNumberMaskFile' 'data/cn2_mask_g1k_b36_chr1.fasta' '-genomeInterval' '1:61699966-61900017' '-configFile' 'conf/genstrip_installtest_parameters.txt'
INFO 11:15:27,868 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVPreprocess-3.out
INFO 11:15:38,836 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeInsertSizeHistograms' '-I' '~/svtoolkit/installtest/test1/metadata/isd/installtest.hist.bin' '-O' '~/svtoolkit/installtest/test1/metadata/isd.hist.bin'
INFO 11:15:38,836 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVPreprocess-5.out
INFO 11:15:48,664 QGraph - 7 Pend, 2 Run, 0 Fail, 3 Done
INFO 11:15:57,863 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' '~/svtoolkit/installtest/test1/metadata/gcprofile/reference.gcprof.zip' '-R' 'data/human_b36_chr1.fasta' '-md' 'test1/metadata' '-writeReferenceProfile' 'true' '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' '-copyNumberMaskFile' 'data/cn2_mask_g1k_b36_chr1.fasta' '-genomeInterval' '1:61699966-61900017' '-configFile' 'conf/genstrip_installtest_parameters.txt'
INFO 11:15:57,869 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeInsertSizeHistograms' '-I' '~/svtoolkit/installtest/test1/metadata/isd/installtest.hist.bin' '-O' '~/svtoolkit/installtest/test1/metadata/isd.hist.bin'
INFO 11:15:57,879 QGraph - Writing incremental jobs reports...
INFO 11:15:57,881 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeInsertStatistics' '-I' '~/svtoolkit/installtest/test1/metadata/isd.hist.bin' '-O' '~/svtoolkit/installtest/test1/metadata/isd.stats.dat'
INFO 11:15:57,882 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVPreprocess-6.out
INFO 11:16:07,220 QGraph - 6 Pend, 1 Run, 0 Fail, 5 Done
INFO 11:16:27,880 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ComputeInsertStatistics' '-I' '~/svtoolkit/installtest/test1/metadata/isd.hist.bin' '-O' '~/svtoolkit/installtest/test1/metadata/isd.stats.dat'
INFO 11:16:28,341 QGraph - Writing incremental jobs reports...
INFO 11:16:28,343 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '~/svtoolkit/installtest/data/human_b36_chr1.fasta' '-I' 'data/installtest.bam' '-O' '~/svtoolkit/installtest/test1/metadata/depth/installtest.depth.txt' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' '-ploidyMapFile' 'data/human_b36_chr1.ploidy.map' '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' '-genomeInterval' '1:61699966-61900017' '-minMapQ' '10' '-insertSizeRadius' '10.0'
INFO 11:16:28,344 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVPreprocess-7.out
INFO 11:16:42,631 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '~/svtoolkit/installtest/data/human_b36_chr1.fasta' '-I' 'data/installtest.bam' '-O' '~/svtoolkit/installtest/test1/metadata/spans/installtest.spans.txt' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' '-maxInsertSizeStandardDeviations' '3'
INFO 11:16:42,631 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVPreprocess-9.out
INFO 11:16:56,312 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '~/svtoolkit/installtest/data/human_b36_chr1.fasta' '-I' 'data/installtest.bam' '-O' '~/svtoolkit/installtest/test1/metadata/gcprofile/installtest.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' '-referenceProfile' 'test1/metadata/gcprofile/reference.gcprof.zip' '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' '-copyNumberMaskFile' 'data/cn2_mask_g1k_b36_chr1.fasta' '-insertSizeRadius' '10.0'
INFO 11:16:56,312 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVPreprocess-11.out
INFO 11:17:17,254 QGraph - 3 Pend, 3 Run, 0 Fail, 6 Done
INFO 11:17:17,259 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadDepthCoverageWalker' '-R' '~/svtoolkit/installtest/data/human_b36_chr1.fasta' '-I' 'data/installtest.bam' '-O' '~/svtoolkit/installtest/test1/metadata/depth/installtest.depth.txt' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' '-ploidyMapFile' 'data/human_b36_chr1.ploidy.map' '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' '-genomeInterval' '1:61699966-61900017' '-minMapQ' '10' '-insertSizeRadius' '10.0'
INFO 11:17:17,264 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeReadSpanCoverageWalker' '-R' '~/svtoolkit/installtest/data/human_b36_chr1.fasta' '-I' 'data/installtest.bam' '-O' '~/svtoolkit/installtest/test1/metadata/spans/installtest.spans.txt' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' '-maxInsertSizeStandardDeviations' '3'
INFO 11:17:17,270 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVCommandLine '-T' 'ComputeGCProfileWalker' '-R' '~/svtoolkit/installtest/data/human_b36_chr1.fasta' '-I' 'data/installtest.bam' '-O' '~/svtoolkit/installtest/test1/metadata/gcprofile/installtest.bam.gcprof.zip' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' '-referenceProfile' 'test1/metadata/gcprofile/reference.gcprof.zip' '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' '-copyNumberMaskFile' 'data/cn2_mask_g1k_b36_chr1.fasta' '-insertSizeRadius' '10.0'
INFO 11:17:17,270 QGraph - Writing incremental jobs reports...
INFO 11:17:17,272 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadDepthCoverage' '-I' '~/svtoolkit/installtest/test1/metadata/depth/installtest.depth.txt' '-O' '~/svtoolkit/installtest/test1/metadata/depth.dat'
INFO 11:17:17,272 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVPreprocess-8.out
INFO 11:17:26,897 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadSpanCoverage' '-I' '~/svtoolkit/installtest/test1/metadata/spans/installtest.spans.txt' '-O' '~/svtoolkit/installtest/test1/metadata/spans.dat'
INFO 11:17:26,897 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVPreprocess-10.out
INFO 11:17:36,722 FunctionEdge - Starting: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeGCProfiles' '-I' '~/svtoolkit/installtest/test1/metadata/gcprofile/installtest.bam.gcprof.zip' '-O' '~/svtoolkit/installtest/test1/metadata/gcprofiles.zip'
INFO 11:17:36,722 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVPreprocess-12.out
INFO 11:17:47,551 QGraph - 0 Pend, 3 Run, 0 Fail, 9 Done
INFO 11:17:47,556 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadDepthCoverage' '-I' '~/svtoolkit/installtest/test1/metadata/depth/installtest.depth.txt' '-O' '~/svtoolkit/installtest/test1/metadata/depth.dat'
INFO 11:17:47,562 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeReadSpanCoverage' '-I' '~/svtoolkit/installtest/test1/metadata/spans/installtest.spans.txt' '-O' '~/svtoolkit/installtest/test1/metadata/spans.dat'
INFO 11:17:47,567 FunctionEdge - Done: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.MergeGCProfiles' '-I' '~/svtoolkit/installtest/test1/metadata/gcprofile/installtest.bam.gcprof.zip' '-O' '~/svtoolkit/installtest/test1/metadata/gcprofiles.zip'
INFO 11:17:47,567 QGraph - Writing incremental jobs reports...
INFO 11:17:47,568 QGraph - 0 Pend, 0 Run, 0 Fail, 12 Done
INFO 11:17:47,570 QCommandLine - Writing final jobs report...
INFO 11:17:47,571 QCommandLine - Script completed successfully with 12 total jobs
INFO 11:17:59,595 QScriptManager - Compiling 2 QScripts
INFO 11:18:28,358 QScriptManager - Compilation complete
INFO 11:18:28,841 HelpFormatter - ----------------------------------------------------------------------
INFO 11:18:28,841 HelpFormatter - Queue v2.5-2-g5671483, Compiled 2013/08/22 15:09:27
INFO 11:18:28,841 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO 11:18:28,841 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:18:28,842 HelpFormatter - Program Args: -S ~/svtoolkit/qscript/SVDiscovery.q -S ~/svtoolkit/qscript/SVQScript.q -gatk ~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar --disableJobReport -cp ~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -disableGATKTraversal -jobLogDir test1/logs -L 1 -minimumSize 100 -maximumSize 1000000 -suppressVCFCommandLines -I data/installtest.bam -O test1.discovery.vcf -run
INFO 11:18:28,842 HelpFormatter - Date/Time: 2015/01/26 11:18:28
INFO 11:18:28,842 HelpFormatter - ----------------------------------------------------------------------
INFO 11:18:28,842 HelpFormatter - ----------------------------------------------------------------------
INFO 11:18:28,860 QCommandLine - Scripting SVDiscovery
INFO 11:18:29,156 QCommandLine - Added 2 functions
INFO 11:18:29,156 QGraph - Generating graph.
INFO 11:18:29,168 QGraph - Running jobs.
INFO 11:18:29,200 FunctionEdge - Starting: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '~/svtoolkit/installtest/data/human_b36_chr1.fasta' '-I' 'data/installtest.bam' '-O' '~/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' '-configFile' 'conf/genstrip_installtest_parameters.txt' '-runDirectory' 'test1' '-genderMapFile' 'data/installtest_gender.map' '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' '-L' '1' '-runFilePrefix' 'test1' '-searchLocus' '1' '-searchWindow' '1' '-searchMinimumSize' '100' '-searchMaximumSize' '1000000'
INFO 11:18:29,201 FunctionEdge - Output written to ~/svtoolkit/installtest/test1/logs/SVDiscovery-1.out
INFO 11:18:47,914 QGraph - 1 Pend, 1 Run, 0 Fail, 0 Done
ERROR 11:18:59,213 FunctionEdge - Error: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '~/svtoolkit/installtest/data/human_b36_chr1.fasta' '-I' 'data/installtest.bam' '-O' '~/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' '-configFile' 'conf/genstrip_installtest_parameters.txt' '-runDirectory' 'test1' '-genderMapFile' 'data/installtest_gender.map' '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' '-L' '1' '-runFilePrefix' 'test1' '-searchLocus' '1' '-searchWindow' '1' '-searchMinimumSize' '100' '-searchMaximumSize' '1000000'
ERROR 11:18:59,247 FunctionEdge - Contents of ~/svtoolkit/installtest/test1/logs/SVDiscovery-1.out:
INFO 11:18:38,694 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:18:38,700 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.5-2-g5671483, Compiled 2013/08/22 15:09:27
INFO 11:18:38,700 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 11:18:38,701 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 11:18:38,706 HelpFormatter - Program Args: -T SVDiscoveryWalker -R ~/svtoolkit/installtest/data/human_b36_chr1.fasta -O ~/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf -disableGATKTraversal true -md test1/metadata -configFile conf/genstrip_installtest_parameters.txt -runDirectory test1 -genderMapFile data/installtest_gender.map -genomeMaskFile data/human_b36_chr1.mask.fasta -L 1 -runFilePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000
INFO 11:18:38,706 HelpFormatter - Date/Time: 2015/01/26 11:18:38
INFO 11:18:38,706 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:18:38,706 HelpFormatter - --------------------------------------------------------------------------------
INFO 11:18:38,987 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:18:39,086 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 11:18:39,108 IntervalUtils - Processing 247249719 bp from intervals
INFO 11:18:39,165 GenomeAnalysisEngine - Creating shard strategy for 0 BAM files
INFO 11:18:39,186 GenomeAnalysisEngine - Done creating shard strategy
INFO 11:18:39,186 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 11:18:39,186 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 11:18:39,186 SVDiscovery - Initializing SVDiscovery ...
INFO 11:18:39,186 SVDiscovery - Reading configuration file ...
INFO 11:18:39,212 SVDiscovery - Read configuration file.
INFO 11:18:39,212 SVDiscovery - Opening reference sequence ...
INFO 11:18:39,213 SVDiscovery - Opened reference sequence.
INFO 11:18:39,213 SVDiscovery - Opening genome mask ...
INFO 11:18:39,214 SVDiscovery - Opened genome mask.
INFO 11:18:39,214 SVDiscovery - Initializing input data set ...
INFO 11:18:39,354 SVDiscovery - Initialized data set: 1 file, 900 read groups, 45 samples.
INFO 11:18:39,355 MetaData - Opening metadata ...
INFO 11:18:39,356 MetaData - Adding metadata directory test1/metadata ...
INFO 11:18:39,376 MetaData - Opened metadata.
INFO 11:18:39,416 SVDiscovery - Opened metadata.
INFO 11:18:39,421 MetaData - Loading insert size histograms ...
INFO 11:18:39,535 SVDiscovery - Discovery alt home filtering is disabled.
INFO 11:18:39,776 SVDiscovery - Processing locus: 1:0-0:100-1000000
INFO 11:18:39,776 SVDiscovery - Locus search window: 1:0-0
INFO 11:18:43,722 SVDiscovery - Processing clusters ...
#INFO: ReadCountAlgorithm: detected metadata version 1, forcing legacy behavior
INFO 11:18:43,947 ReadCountDiskCache - Initializing read count disk cache [test1/metadata/rccache.bin] ...
INFO 11:18:43,949 ReadCountDiskCache - Read count disk cache: no cache files found.
INFO 11:18:43,949 SVDiscovery - Initializing memory-mapped read count caching
INFO 11:18:43,957 SVDiscovery - No hapmap snp genotype directory specified
INFO 11:18:43,958 SVDiscovery - No array intensity data specified
INFO 11:18:44,131 SVDiscovery - Clustering: Generating clusters for 6 read pairs.
INFO 11:18:44,132 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
INFO 11:18:44,132 SVDiscovery - Processing cluster 1:61722491-61722556 1:61723000-61723144 LR 6
#ERROR: ClusterDepthModule.computePValue 74 35506 511 321006
Error: Exception processing cluster: Error running script ~/svtoolkit/R/discovery/compute_depth_pvalue.R: During startup - Warning message:
Setting LC_CTYPE failed, using "C"
0.035584

Cluster: 1:61722491-61722556 1:61723000-61723144 LR 6
INFO 11:18:47,832 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
INFO 11:18:47,844 HttpMethodDirector - Retrying request
INFO 11:18:47,846 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
INFO 11:18:47,846 HttpMethodDirector - Retrying request
INFO 11:18:47,847 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
INFO 11:18:47,847 HttpMethodDirector - Retrying request
INFO 11:18:47,848 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
INFO 11:18:47,848 HttpMethodDirector - Retrying request
INFO 11:18:47,849 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Network is unreachable
INFO 11:18:47,849 HttpMethodDirector - Retrying request
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Error running script ~/svtoolkit/R/discovery/compute_depth_pvalue.R: During startup - Warning message:
Setting LC_CTYPE failed, using "C"
0.035584

at org.broadinstitute.sv.discovery.ClusterDepthModule.computePValue(ClusterDepthModule.java:240)
at org.broadinstitute.sv.discovery.ClusterDepthModule.computeDepth(ClusterDepthModule.java:179)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:440)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:357)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:196)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:109)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:42)
at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:123)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:125)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:79)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.5-2-g5671483):
##### ERROR
##### ERROR Please check the documentation guide to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Error running script ~/svtoolkit/R/discovery/compute_depth_pvalue.R: During startup - Warning message:
##### ERROR Setting LC_CTYPE failed, using "C"
##### ERROR 0.035584
##### ERROR ------------------------------------------------------------------------------------------
INFO 11:18:59,249 QGraph - Writing incremental jobs reports...
INFO 11:18:59,249 QGraph - 1 Pend, 0 Run, 1 Fail, 0 Done
INFO 11:18:59,251 QCommandLine - Writing final jobs report...
INFO 11:18:59,251 QCommandLine - Done with errors
INFO 11:18:59,253 QGraph - -------
INFO 11:18:59,255 QGraph - Failed: 'java' '-Xmx4096m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=~/svtoolkit/installtest/tmpdir' '-cp' '~/svtoolkit/lib/SVToolkit.jar:~/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:~/svtoolkit/lib/gatk/Queue.jar' org.broadinstitute.sv.main.SVDiscovery '-T' 'SVDiscoveryWalker' '-R' '~/svtoolkit/installtest/data/human_b36_chr1.fasta' '-I' 'data/installtest.bam' '-O' '~/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf' '-disableGATKTraversal' 'true' '-md' 'test1/metadata' '-configFile' 'conf/genstrip_installtest_parameters.txt' '-runDirectory' 'test1' '-genderMapFile' 'data/installtest_gender.map' '-genomeMaskFile' 'data/human_b36_chr1.mask.fasta' '-L' '1' '-runFilePrefix' 'test1' '-searchLocus' '1' '-searchWindow' '1' '-searchMinimumSize' '100' '-searchMaximumSize' '1000000'
INFO 11:18:59,265 QGraph - Log: ~/svtoolkit/installtest/test1/logs/SVDiscovery-1.out
INFO 11:18:59,266 QCommandLine - Script failed with 2 total jobs