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A partical error for CNV_Stage7 .

SunhyeSunhye KoreaMember
edited July 2015 in GenomeSTRiP

Hi.
I use GenomeSTRiP2.0, release of r1599, to call SV and CNV .

I encountered a partical error during CNV_Stage7.

    INFO  10:03:48,179 HelpFormatter - Date/Time: 2015/07/08 10:03:48 
    INFO  10:03:48,180 HelpFormatter - ------------------------------------------------------------------ 
    INFO  10:03:48,180 HelpFormatter - ------------------------------------------------------------------ 
    INFO  10:03:48,204 RefineCNVBoundaries - Opening reference sequence ... 
    INFO  10:03:48,206 RefineCNVBoundaries - Opened reference sequence. 
    INFO  10:03:48,206 RefineCNVBoundaries - Opening genome mask ... 
    INFO  10:03:48,208 RefineCNVBoundaries - Opened genome mask. 
    INFO  10:03:48,210 MetaData - Opening metadata ...  
    INFO  10:03:48,218 MetaData - Adding metadata directory Sample_Wgs_Work_0701/metadata ... 
    INFO  10:03:48,247 MetaData - Opened metadata. 
    INFO  10:03:48,257 RefineCNVBoundaries - Initializing input data set ... 
    INFO  10:03:48,329 RefineCNVBoundaries - Initialized data set: 1 file, 490 read groups, 40 samples. 
    INFO  10:03:48,514 ReadCountDiskCache - Initializing read count disk cache [Sample_Wgs_Work_0701/metadata/rccache.bin] ... 
    INFO  10:03:48,515 ReadCountDiskCache - Initialized read count disk cache with 1 file. 
    Exception in thread "main" java.lang.RuntimeException: EM estep failed correction: 40 40.33333333333334
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
        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.runAndReturnResult(CommandLineProgram.java:29)
        at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
        at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.main(RefineCNVBoundaries.java:128)
    Caused by: java.lang.RuntimeException: EM estep failed correction: 40 40.33333333333334
        at org.broadinstitute.sv.genotyping.GenotypingEMAlgorithm$EMRun.estep(GenotypingEMAlgorithm.java:431)
        at org.broadinstitute.sv.genotyping.GenotypingEMAlgorithm$EMRun.run(GenotypingEMAlgorithm.java:236)
        at org.broadinstitute.sv.genotyping.GenotypingEMAlgorithm.computeMixtureModel(GenotypingEMAlgorithm.java:87)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeMixtureModelInternal(GenotypingDepthModule.java:983)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeMixtureModel(GenotypingDepthModule.java:900)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.genotypeCnp(GenotypingDepthModule.java:158)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.genotypeCnp(BoundaryRefinementAlgorithm.java:270)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineOneBoundary(BoundaryRefinementAlgorithm.java:616)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaryStep(BoundaryRefinementAlgorithm.java:545)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaries(BoundaryRefinementAlgorithm.java:519)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.processVariant(BoundaryRefinementAlgorithm.java:223)
        at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.run(RefineCNVBoundaries.java:207)
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
        ... 5 more 
    INFO  10:04:08,911 QGraph - Writing incremental jobs reports... 
    INFO  10:04:08,935 QGraph - 4 Pend, 0 Run, 1 Fail, 833 Done 
    INFO  10:04:08,943 QCommandLine - Writing final jobs report... 
    INFO  10:04:08,944 QCommandLine - Done with errors 
    INFO  10:04:08,974 QGraph - ------- 
    INFO  10:04:08,975 QGraph - Failed:   'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.genotyping.RefineCNVBoundaries'  '-I' '/BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam'  '-O' '/BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged.brig.vcf'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-md' 'Sample_Wgs_Work_0701/metadata'  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-P' 'depth.readCountCacheIgnoreGenomeMask:true'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta'  '-genderMapFile' './WGS.gender.map'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt'  '-vcf' 'Sample_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz'  '-site' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729.sites.list'  '-auxFilePrefix' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged'  '-boundaryPrecision' '100'  '-minimumRefinedLength' '500'  '-maximumReferenceGapLength' '1000'  
    INFO  10:04:08,975 QGraph - Log:     /BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage7/seq_4/logs/CNVDiscoveryStage7-730.out 
    INFO  10:04:08,976 QCommandLine - Script failed: 4 Pend, 0 Run, 1 Fail, 833 Done  
    INFO  10:01:23,497 QGraph - Writing incremental jobs reports... 
    INFO  10:01:23,499 QGraph - 5 Pend, 0 Run, 1 Fail, 239 Done 
    INFO  10:01:23,503 QCommandLine - Writing final jobs report... 
    INFO  10:01:23,504 QCommandLine - Done with errors 
    INFO  10:01:23,518 QGraph - ------- 
    INFO  10:01:23,520 QGraph - Failed:   'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.gatk.queue.QCommandLine'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage7.q'  '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q' '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q'  '-S' '/BiO/psh/tools/svtoolkit/qscript/SVQScript.q'  '-gatk' '/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar'  '-jobLogDir' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/logs'  '-memLimit' '2.0'  '-jobRunner' 'Drmaa'  '-gatkJobRunner' 'Drmaa'  '-jobNative' '-v SV_DIR'  -run  '-sequenceName' '4'  '-runDirectory' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4'  '-sentinelFile' 'Sample_Wgs_Work_0701/cnv_sentinel_files/stage_7_seq_4.sent'  --disableJobReport  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta'  '-copyNumberMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.gcmask.fasta'  '-readDepthMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.rdmask.bed'  '-genderMaskBedFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.gendermask.bed'  '-vdjBedFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.vdjregions.bed'  '-genderMapFile' './WGS.gender.map'  '-md' 'Sample_Wgs_Work_0701/metadata'  -disableGATKTraversal  '-I' 'Sample_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam'  '-vcf' 'Sample_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz'  '-siteListFile' 'Sample_Wgs_Work_0701/cnv_stage6/seq_4/eval/SelectedVariants.list'  '-boundaryPrecision' '100'  '-maximumReferenceGapLength' '1000'  '-minimumRefinedLength' '500'  '-brigSiteVcfFile' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/seq_4.brig.sites.vcf.gz'  -produceAuxiliaryFiles  
    INFO  10:01:23,520 QGraph - Log:     /BiO/psh/Project/sv/Sample_Wgs_Work_0701/logs/CNVDiscoveryPipeline-126.out 
    INFO  10:01:23,522 QCommandLine - Script failed: 5 Pend, 0 Run, 1 Fail, 239 Done 

So This run was stopped at CNV_stage11.

in cnv_sentinal

[email protected]:/BiO/psh/Project/sv/sample_Wgs_Work_0701/cnv_sentinel_files$ lh .*.fail
-rw-rw-r-- 1 sunhye sunhye 0  7??  8 10:01 .stage_7_seq_4.sent.fail
[email protected]:/BiO/psh/Project/sv/sample_Wgs_Work_0701/cnv_sentinel_files$ lh .stage_11*
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:15 .stage_11_seq_10.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:13 .stage_11_seq_11.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:06 .stage_11_seq_12.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:02 .stage_11_seq_13.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:05 .stage_11_seq_14.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:07 .stage_11_seq_15.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:09 .stage_11_seq_16.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:14 .stage_11_seq_17.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:02 .stage_11_seq_18.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:07 .stage_11_seq_19.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:33 .stage_11_seq_1.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:03 .stage_11_seq_20.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 17:59 .stage_11_seq_21.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:05 .stage_11_seq_22.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:20 .stage_11_seq_2.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:07 .stage_11_seq_3.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:15 .stage_11_seq_5.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:14 .stage_11_seq_6.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:20 .stage_11_seq_7.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:14 .stage_11_seq_8.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:16 .stage_11_seq_9.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 18:01 .stage_11_seq_X.sent.done
-rw-r--r-- 1 sunhye sunhye 0  7??  7 17:59 .stage_11_seq_Y.sent.done

[email protected]:/BiO/psh/Project/sv/sample_Wgs_Work_0701/cnv_sentinel_files$ ls .*seq_4*
.stage_1_seq_4.sent.done  .stage_3_seq_4.sent.done  .stage_6_seq_4.sent.done
.stage_2_seq_4.sent.done  .stage_4_seq_4.sent.done  .stage_7_seq_4.sent.fail

How do I fix this bug?

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Best Answers

Answers

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    I will need a reproducible test case to debug this problem.

    One possible way you can try to help me reproduce it is like this:
    1. From the log files, dig out the command for RefineCNVBoundaries that is failing.
    2. Rerun the command, but add two parameters:
    -debug true
    -P depth.writeModelInputs:true

    The first should enable printing out the different intervals being tested by the hill climbing algorithm.
    The second should cause some files to be written in rundir/depth/interval.depth.dat.
    If you can send me the last one of these depth.dat files written, the one that corresponds to the last interval tested before the error, I think I will be able to debug the problem.

  • SunhyeSunhye KoreaMember
    edited July 2015

    Hi, Bob
    the command for RefineCNVBoundaries is

    -I /BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam -O /BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged.brig.vcf -R /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta -md Sample_Wgs_Work_0701/metadata -configFile /BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt -P depth.readCountCacheIgnoreGenomeMask:true -genomeMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta -genomeMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta -genderMapFile ./WGS.gender.map -ploidyMapFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt -vcf Sample_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz -site Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729.sites.list -auxFilePrefix Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged -boundaryPrecision 100 -minimumRefinedLength 500 -maximumReferenceGapLength 1000 
    

    I rerun, which add 2 parameter that you propose above comment to my script.
    In error

    SVToolkit version 2.00 (build 1599)
    Build date: 2015/06/29 15:05:43
    Web site: http://www.broadinstitute.org/software/genomestrip
    INFO  14:00:59,892 QScriptManager - Compiling 2 QScripts 
    INFO  14:01:22,678 QScriptManager - Compilation complete 
    INFO  14:01:22,884 HelpFormatter - ---------------------------------------------------------------------- 
    INFO  14:01:22,884 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/05/15 09:12:56 
    INFO  14:01:22,885 HelpFormatter - Copyright (c) 2012 The Broad Institute 
    INFO  14:01:22,885 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
    INFO  14:01:22,886 HelpFormatter - Program Args: -jobNative -v SV_DIR -S /BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryPipeline.q -S /BiO/psh/tools/svtoolkit/qscript/SVQScript.q -gatk /BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar -configFile /BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt -tempDir ./tmpdir -R /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta -runDirectory Sample_Wgs_Work_0701 -md Sample_Wgs_Work_0701/metadata -jobLogDir Sample_Wgs_Work_0701/logs -ploidyMapFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt -genderMapFile ./WGS.gender.map -genomeMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta -tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 -minimumRefinedLength 500 -produceAuxiliaryFiles -I wgs.sample.sort.list -jobRunner Drmaa -gatkJobRunner Drmaa --disableJobReport -debug true -P depth.writeModelInputs:true -run 
    INFO  14:01:22,892 HelpFormatter - Executing as [email protected] on Linux 3.16.0-031600-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14. 
    INFO  14:01:22,893 HelpFormatter - Date/Time: 2015/07/08 14:01:22 
    INFO  14:01:22,893 HelpFormatter - ---------------------------------------------------------------------- 
    INFO  14:01:22,893 HelpFormatter - ---------------------------------------------------------------------- 
    INFO  14:01:22,916 QCommandLine - Scripting CNVDiscoveryPipeline 
    INFO  14:01:24,144 QCommandLine - Added 245 functions 
    INFO  14:01:24,145 QGraph - Generating graph. 
    INFO  14:01:24,335 QGraph - Running jobs. 
    INFO  14:01:24,705 FunctionEdge - Starting:  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.gatk.queue.QCommandLine'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage7.q'  '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q' '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q'  '-S' '/BiO/psh/tools/svtoolkit/qscript/SVQScript.q'  '-gatk' '/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar'  '-jobLogDir' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/logs'  '-memLimit' '2.0'  '-jobRunner' 'Drmaa'  '-gatkJobRunner' 'Drmaa'  '-jobNative' '-v SV_DIR'  -run  '-sequenceName' '4'  '-runDirectory' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4'  '-sentinelFile' 'Sample_Wgs_Work_0701/cnv_sentinel_files/stage_7_seq_4.sent'  --disableJobReport  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-P' 'depth.writeModelInputs:true'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta'  '-copyNumberMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.gcmask.fasta'  '-readDepthMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.rdmask.bed'  '-genderMaskBedFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.gendermask.bed'  '-vdjBedFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.vdjregions.bed'  '-genderMapFile' './WGS.gender.map'  '-md' 'Sample_Wgs_Work_0701/metadata'  -disableGATKTraversal  '-I' 'Sample_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam'  '-vcf' 'Sample_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz'  '-siteListFile' 'Sample_Wgs_Work_0701/cnv_stage6/seq_4/eval/SelectedVariants.list'  '-boundaryPrecision' '100'  '-maximumReferenceGapLength' '1000'  '-minimumRefinedLength' '500'  '-brigSiteVcfFile' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/seq_4.brig.sites.vcf.gz'  -produceAuxiliaryFiles  
    INFO  14:01:24,706 FunctionEdge - Output written to /BiO/psh/Project/sv/Sample_Wgs_Work_0701/logs/CNVDiscoveryPipeline-126.out 
    INFO  14:01:24,753 DrmaaJobRunner - Submitted job id: 93565 
    INFO  14:01:24,757 QGraph - 5 Pend, 1 Run, 0 Fail, 239 Done 
    ERROR 14:02:54,710 FunctionEdge - Error:  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.gatk.queue.QCommandLine'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage7.q'  '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q' '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q'  '-S' '/BiO/psh/tools/svtoolkit/qscript/SVQScript.q'  '-gatk' '/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar'  '-jobLogDir' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/logs'  '-memLimit' '2.0'  '-jobRunner' 'Drmaa'  '-gatkJobRunner' 'Drmaa'  '-jobNative' '-v SV_DIR'  -run  '-sequenceName' '4'  '-runDirectory' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4'  '-sentinelFile' 'Sample_Wgs_Work_0701/cnv_sentinel_files/stage_7_seq_4.sent'  --disableJobReport  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-P' 'depth.writeModelInputs:true'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta'  '-copyNumberMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.gcmask.fasta'  '-readDepthMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.rdmask.bed'  '-genderMaskBedFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.gendermask.bed'  '-vdjBedFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.vdjregions.bed'  '-genderMapFile' './WGS.gender.map'  '-md' 'Sample_Wgs_Work_0701/metadata'  -disableGATKTraversal  '-I' 'Sample_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam'  '-vcf' 'Sample_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz'  '-siteListFile' 'Sample_Wgs_Work_0701/cnv_stage6/seq_4/eval/SelectedVariants.list'  '-boundaryPrecision' '100'  '-maximumReferenceGapLength' '1000'  '-minimumRefinedLength' '500'  '-brigSiteVcfFile' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/seq_4.brig.sites.vcf.gz'  -produceAuxiliaryFiles  
    ERROR 14:02:54,715 FunctionEdge - Contents of /BiO/psh/Project/sv/Sample_Wgs_Work_0701/logs/CNVDiscoveryPipeline-126.out:
    INFO  14:04:56,939 QScriptManager - Compiling 4 QScripts 
    INFO  14:05:08,433 QScriptManager - Compilation complete 
    INFO  14:05:08,586 HelpFormatter - ---------------------------------------------------------------------- 
    INFO  14:05:08,587 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/05/15 09:12:56 
    INFO  14:05:08,587 HelpFormatter - Copyright (c) 2012 The Broad Institute 
    INFO  14:05:08,587 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
    INFO  14:05:08,588 HelpFormatter - Program Args: -cp /BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar -S /BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage7.q -S /BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q -S /BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q -S /BiO/psh/tools/svtoolkit/qscript/SVQScript.q -gatk /BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -jobLogDir Sample_Wgs_Work_0701/cnv_stage7/seq_4/logs -memLimit 2.0 -jobRunner Drmaa -gatkJobRunner Drmaa -jobNative -v SV_DIR -run -sequenceName 4 -runDirectory Sample_Wgs_Work_0701/cnv_stage7/seq_4 -sentinelFile Sample_Wgs_Work_0701/cnv_sentinel_files/stage_7_seq_4.sent --disableJobReport -configFile /BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt -P depth.writeModelInputs:true -R /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta -ploidyMapFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt -genomeMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta -genomeMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta -copyNumberMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.gcmask.fasta -readDepthMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.rdmask.bed -genderMaskBedFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.gendermask.bed -vdjBedFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.vdjregions.bed -genderMapFile ./WGS.gender.map -md Sample_Wgs_Work_0701/metadata -disableGATKTraversal -I Sample_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam -vcf Sample_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz -siteListFile Sample_Wgs_Work_0701/cnv_stage6/seq_4/eval/SelectedVariants.list -boundaryPrecision 100 -maximumReferenceGapLength 1000 -minimumRefinedLength 500 -brigSiteVcfFile Sample_Wgs_Work_0701/cnv_stage7/seq_4/seq_4.brig.sites.vcf.gz -produceAuxiliaryFiles 
    INFO  14:05:08,588 HelpFormatter - Executing as [email protected] on Linux 3.16.0-031600-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_25-b17. 
    INFO  14:05:08,589 HelpFormatter - Date/Time: 2015/07/08 14:05:08 
    INFO  14:05:08,589 HelpFormatter - ---------------------------------------------------------------------- 
    INFO  14:05:08,589 HelpFormatter - ---------------------------------------------------------------------- 
    INFO  14:05:08,599 QCommandLine - Scripting CNVDiscoveryStage7 
    INFO  14:05:12,968 QCommandLine - Added 838 functions 
    INFO  14:05:12,969 QGraph - Generating graph. 
    INFO  14:05:13,104 QGraph - Running jobs. 
    INFO  14:05:13,364 FunctionEdge - Starting:  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.genotyping.RefineCNVBoundaries'  '-I' '/BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam'  '-O' '/BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged.brig.vcf'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-md' 'Sample_Wgs_Work_0701/metadata'  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-P' 'depth.readCountCacheIgnoreGenomeMask:true'  '-P' 'depth.writeModelInputs:true'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta'  '-genderMapFile' './WGS.gender.map'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt'  '-vcf' 'Sample_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz'  '-site' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729.sites.list'  '-auxFilePrefix' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged'  '-boundaryPrecision' '100'  '-minimumRefinedLength' '500'  '-maximumReferenceGapLength' '1000'  
    INFO  14:05:13,365 FunctionEdge - Output written to /BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage7/seq_4/logs/CNVDiscoveryStage7-730.out 
    INFO  14:05:13,426 DrmaaJobRunner - Submitted job id: 93566 
    INFO  14:05:13,430 QGraph - 4 Pend, 1 Run, 0 Fail, 833 Done 
    ERROR 14:05:43,378 FunctionEdge - Error:  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.genotyping.RefineCNVBoundaries'  '-I' '/BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam'  '-O' '/BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged.brig.vcf'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-md' 'Sample_Wgs_Work_0701/metadata'  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-P' 'depth.readCountCacheIgnoreGenomeMask:true'  '-P' 'depth.writeModelInputs:true'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta'  '-genderMapFile' './WGS.gender.map'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt'  '-vcf' 'Sample_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz'  '-site' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729.sites.list'  '-auxFilePrefix' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged'  '-boundaryPrecision' '100'  '-minimumRefinedLength' '500'  '-maximumReferenceGapLength' '1000'  
    ERROR 14:05:43,383 FunctionEdge - Contents of /BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage7/seq_4/logs/CNVDiscoveryStage7-730.out:
    INFO  14:05:24,384 HelpFormatter - ------------------------------------------------------------------ 
    INFO  14:05:24,833 HelpFormatter - Program Name: org.broadinstitute.sv.genotyping.RefineCNVBoundaries 
    INFO  14:05:24,842 HelpFormatter - Program Args: -I /BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam -O /BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged.brig.vcf -R /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta -md Sample_Wgs_Work_0701/metadata -configFile /BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt -P depth.readCountCacheIgnoreGenomeMask:true -P depth.writeModelInputs:true -genomeMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta -genomeMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta -genderMapFile ./WGS.gender.map -ploidyMapFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt -vcf Sample_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz -site Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729.sites.list -auxFilePrefix Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged -boundaryPrecision 100 -minimumRefinedLength 500 -maximumReferenceGapLength 1000 
    INFO  14:05:24,848 HelpFormatter - Executing as [email protected] on Linux 3.16.0-031600-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_25-b17. 
    INFO  14:05:24,848 HelpFormatter - Date/Time: 2015/07/08 14:05:24 
    INFO  14:05:24,848 HelpFormatter - ------------------------------------------------------------------ 
    INFO  14:05:24,848 HelpFormatter - ------------------------------------------------------------------ 
    INFO  14:05:25,973 RefineCNVBoundaries - Opening reference sequence ... 
    INFO  14:05:26,594 RefineCNVBoundaries - Opened reference sequence. 
    INFO  14:05:26,594 RefineCNVBoundaries - Opening genome mask ... 
    INFO  14:05:27,265 RefineCNVBoundaries - Opened genome mask. 
    INFO  14:05:27,267 MetaData - Opening metadata ...  
    INFO  14:05:27,356 MetaData - Adding metadata directory Sample_Wgs_Work_0701/metadata ... 
    INFO  14:05:27,994 MetaData - Opened metadata. 
    INFO  14:05:28,191 RefineCNVBoundaries - Initializing input data set ... 
    INFO  14:05:28,277 RefineCNVBoundaries - Initialized data set: 1 file, 490 read groups, 40 samples. 
    INFO  14:05:28,468 ReadCountDiskCache - Initializing read count disk cache [Sample_Wgs_Work_0701/metadata/rccache.bin] ... 
    INFO  14:05:28,469 ReadCountDiskCache - Initialized read count disk cache with 1 file. 
    Exception in thread "main" java.lang.RuntimeException: EM estep failed correction: 40 40.33333333333334
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
        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.runAndReturnResult(CommandLineProgram.java:29)
        at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
        at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.main(RefineCNVBoundaries.java:128)
    Caused by: java.lang.RuntimeException: EM estep failed correction: 40 40.33333333333334
        at org.broadinstitute.sv.genotyping.GenotypingEMAlgorithm$EMRun.estep(GenotypingEMAlgorithm.java:431)
        at org.broadinstitute.sv.genotyping.GenotypingEMAlgorithm$EMRun.run(GenotypingEMAlgorithm.java:236)
        at org.broadinstitute.sv.genotyping.GenotypingEMAlgorithm.computeMixtureModel(GenotypingEMAlgorithm.java:87)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeMixtureModelInternal(GenotypingDepthModule.java:983)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeMixtureModel(GenotypingDepthModule.java:900)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.genotypeCnp(GenotypingDepthModule.java:158)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.genotypeCnp(BoundaryRefinementAlgorithm.java:270)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineOneBoundary(BoundaryRefinementAlgorithm.java:616)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaryStep(BoundaryRefinementAlgorithm.java:545)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaries(BoundaryRefinementAlgorithm.java:519)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.processVariant(BoundaryRefinementAlgorithm.java:223)
        at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.run(RefineCNVBoundaries.java:207)
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
        ... 5 more 
    INFO  14:05:43,384 QGraph - Writing incremental jobs reports... 
    INFO  14:05:43,405 QGraph - 4 Pend, 0 Run, 1 Fail, 833 Done 
    INFO  14:05:43,413 QCommandLine - Writing final jobs report... 
    INFO  14:05:43,414 QCommandLine - Done with errors 
    INFO  14:05:43,458 QGraph - ------- 
    INFO  14:05:43,463 QGraph - Failed:   'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.genotyping.RefineCNVBoundaries'  '-I' '/BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam'  '-O' '/BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged.brig.vcf'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-md' 'Sample_Wgs_Work_0701/metadata'  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-P' 'depth.readCountCacheIgnoreGenomeMask:true'  '-P' 'depth.writeModelInputs:true'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta'  '-genderMapFile' './WGS.gender.map'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt'  '-vcf' 'Sample_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz'  '-site' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729.sites.list'  '-auxFilePrefix' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged'  '-boundaryPrecision' '100'  '-minimumRefinedLength' '500'  '-maximumReferenceGapLength' '1000'  
    INFO  14:05:43,464 QGraph - Log:     /BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage7/seq_4/logs/CNVDiscoveryStage7-730.out 
    INFO  14:05:43,470 QCommandLine - Script failed: 4 Pend, 0 Run, 1 Fail, 833 Done  
    INFO  14:02:54,717 QGraph - Writing incremental jobs reports... 
    INFO  14:02:54,721 QGraph - 5 Pend, 0 Run, 1 Fail, 239 Done 
    INFO  14:02:54,725 QCommandLine - Writing final jobs report... 
    INFO  14:02:54,727 QCommandLine - Done with errors 
    INFO  14:02:54,759 QGraph - ------- 
    INFO  14:02:54,762 QGraph - Failed:   'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.gatk.queue.QCommandLine'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage7.q'  '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q' '-S' '/BiO/psh/tools/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q'  '-S' '/BiO/psh/tools/svtoolkit/qscript/SVQScript.q'  '-gatk' '/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar'  '-jobLogDir' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/logs'  '-memLimit' '2.0'  '-jobRunner' 'Drmaa'  '-gatkJobRunner' 'Drmaa'  '-jobNative' '-v SV_DIR'  -run  '-sequenceName' '4'  '-runDirectory' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4'  '-sentinelFile' 'Sample_Wgs_Work_0701/cnv_sentinel_files/stage_7_seq_4.sent'  --disableJobReport  '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt'  '-P' 'depth.writeModelInputs:true'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt'  '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta'  '-copyNumberMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.gcmask.fasta'  '-readDepthMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.rdmask.bed'  '-genderMaskBedFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.gendermask.bed'  '-vdjBedFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.vdjregions.bed'  '-genderMapFile' './WGS.gender.map'  '-md' 'Sample_Wgs_Work_0701/metadata'  -disableGATKTraversal  '-I' 'Sample_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam'  '-vcf' 'Sample_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz'  '-siteListFile' 'Sample_Wgs_Work_0701/cnv_stage6/seq_4/eval/SelectedVariants.list'  '-boundaryPrecision' '100'  '-maximumReferenceGapLength' '1000'  '-minimumRefinedLength' '500'  '-brigSiteVcfFile' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/seq_4.brig.sites.vcf.gz'  -produceAuxiliaryFiles  
    INFO  14:02:54,763 QGraph - Log:     /BiO/psh/Project/sv/Sample_Wgs_Work_0701/logs/CNVDiscoveryPipeline-126.out 
    INFO  14:02:54,764 QCommandLine - Script failed: 5 Pend, 0 Run, 1 Fail, 239 Done   
    

    Then, I check rundir/depth/interval.depth.dat.
    But depth directory is not in rundir but in rundir/metadata directory , and there are *.depth.txt files created by SVPreprocessing.q.
    *depth.txt extentions files aren't in rundir, anywhere.

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    No, you misunderstand.

    Try to run this command (sorry about the formatting and you could remove most of the quotes):
    'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir' '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar' '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.genotyping.RefineCNVBoundaries' '-I' '/BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam' '-O' '/BiO/psh/Project/sv/Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged.brig.vcf' '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta' '-md' 'Sample_Wgs_Work_0701/metadata' '-configFile' '/BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt' '-P' 'depth.readCountCacheIgnoreGenomeMask:true' '-P' 'depth.writeModelInputs:true' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta' '-genomeMaskFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta' '-genderMapFile' './WGS.gender.map' '-ploidyMapFile' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt' '-vcf' 'Sample_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz' '-site' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729.sites.list' '-auxFilePrefix' 'Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged' '-boundaryPrecision' '100' '-minimumRefinedLength' '500' '-maximumReferenceGapLength' '1000' -debug true -P depth.writeModelInputs:true

    and then also look in Sample_Wgs_Work_0701/cnv_stage7/seq_4/P0729/depth

  • SunhyeSunhye KoreaMember
    edited July 2015

    Hi, bob
    I'm not sure that I understand that you are saying.
    but, I attempt to your advise.

    I run that.

    java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir  -cp /BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar  -cp /BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar  org.broadinstitute.sv.genotyping.RefineCNVBoundaries  -I /BiO/psh/Project/sv/KPGP_Wgs_Work_0701/cnv_stage6/seq_4/seq_4.merged_headers.bam  -O /BiO/psh/Project/sv/KPGP_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged.brig.vcf  -R /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta  -md KPGP_Wgs_Work_0701/metadata  -configFile /BiO/psh/tools/svtoolkit/conf/genstrip_parameters.txt  -P depth.readCountCacheIgnoreGenomeMask:true  -P depth.writeModelInputs:true  -genomeMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.svmask.fasta -genomeMaskFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.lcmask.fasta  -genderMapFile ./WGS.gender.map  -ploidyMapFile /BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.ploidymap.txt  -vcf KPGP_Wgs_Work_0701/cnv_stage4/seq_4/seq_4.merged.genotypes.vcf.gz  -site KPGP_Wgs_Work_0701/cnv_stage7/seq_4/P0729.sites.list  -auxFilePrefix KPGP_Wgs_Work_0701/cnv_stage7/seq_4/P0729/seq_4.merged  -boundaryPrecision 100  -minimumRefinedLength 500  -maximumReferenceGapLength 1000 -debug true -P depth.writeModelInputs:true
    

    And stdout was shown.

    #DBG: refine CNV_4_173429108_173430246 LEFT RIGHT try 3: 4:173429746-173430812 0.8700291486784686
    #DBG: BoundaryRefinement / genotype CNP CNV_4_173429108_173430246 @ 4:173429885-173430812 ...
    INFO  17:03:39,540 GenotypingModuleBase - GenotypingDepthModule processing site CNV_4_173429108_173430246_4:173429885-173430812 ... 
    INFO  17:03:39,542 GenotypingModuleBase - Computing expected counts ... 
    INFO  17:03:39,561 GenotypingModuleBase - Computing expected counts done. 
    INFO  17:03:39,562 GenotypingModuleBase - Computing effective length ... 
    INFO  17:03:39,562 GenotypingModuleBase - specifiedMixtureModel=null 
    INFO  17:03:39,562 GenotypingModuleBase - Computing mixture model for CNV_4_173429108_173430246_4:173429885-173430812 ... 
    Exception in thread "main" java.lang.RuntimeException: EM estep failed correction: 40 40.33333333333334
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
        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.runAndReturnResult(CommandLineProgram.java:29)
        at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
        at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.main(RefineCNVBoundaries.java:128)
    Caused by: java.lang.RuntimeException: EM estep failed correction: 40 40.33333333333334
        at org.broadinstitute.sv.genotyping.GenotypingEMAlgorithm$EMRun.estep(GenotypingEMAlgorithm.java:431)
        at org.broadinstitute.sv.genotyping.GenotypingEMAlgorithm$EMRun.run(GenotypingEMAlgorithm.java:236)
        at org.broadinstitute.sv.genotyping.GenotypingEMAlgorithm.computeMixtureModel(GenotypingEMAlgorithm.java:87)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeMixtureModelInternal(GenotypingDepthModule.java:983)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeMixtureModel(GenotypingDepthModule.java:900)
        at org.broadinstitute.sv.genotyping.GenotypingDepthModule.genotypeCnp(GenotypingDepthModule.java:158)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.genotypeCnp(BoundaryRefinementAlgorithm.java:270)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineOneBoundary(BoundaryRefinementAlgorithm.java:616)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaryStep(BoundaryRefinementAlgorithm.java:545)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaries(BoundaryRefinementAlgorithm.java:519)
        at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.processVariant(BoundaryRefinementAlgorithm.java:223)
        at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.run(RefineCNVBoundaries.java:207)
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
        ... 5 more
    

    less ./cnv_stage7/seq_4/P0729/depth/CNV_4_173429108_173430246_4:173429885-173430812

    SAMPLE  COUNT   EXPECTED
    sample-00001      0.0     61.53129062548544
    sample-00002      0.0     60.811172369700074
    sample-00003      0.0     71.91703598509744
    sample-00005      1.0     56.34037077889613
    sample-00006      0.0     58.52542217060812
    sample-00032      0.0     76.14583048324387
    sample-00033      0.0     68.45901202465163
    sample-00039      0.0     58.095156302156994
    sample-00117      0.0     71.83564586346718
    sample-00120      0.0     74.23538096307328
    sample-00121      0.0     76.05707501538728
    sample-00122      0.0     66.59745060641374
    sample-00124      0.0     71.88282587643366
    sample-00125      0.0     80.75229452967505
    sample-00127      0.0     80.82943152569416
    sample-00128      0.0     76.5258272916819
    sample-00129      0.0     65.56614555602428
    sample-00131      0.0     76.46163329041684
    sample-00132      0.0     79.57163138261468
    sample-00134      0.0     73.4271592613424
    sample-00136      0.0     71.48172834863945
    sample-00137      0.0     74.9413335286491
    sample-00138      0.0     77.37393652401288
    sample-00139      0.0     66.13467313821623
    sample-00142      0.0     84.95691019358749
    sample-00144      0.0     86.76075562456288
    sample-00145      0.0     73.4469649160416
    sample-00219      0.0     72.84003611686924
    sample-00220      0.0     67.58809613634382
    sample-00221      0.0     64.42725454420507
    sample-00224      0.0     62.7374168048015
    sample-00227      0.0     76.98952571560919
    sample-00228      0.0     76.40930660527286
    sample-00229      0.0     74.39934753108531
    sample-00230      0.0     71.90516349816068
    sample-00231      0.0     70.33880015676814
    sample-00232      0.0     72.64859990261264
    sample-00233      0.0     69.69578938699556
    sample-00234      0.0     73.94402818587483
    sample-00235      0.0     71.42731477346973
    

    My samples are 62 individuals but this file's samples are only 40 individuals.
    Is this associated with error in cnv_stage7_seq4?
    Otherwise, why are some samples omitted some samples?

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    That's perfect.

    In stage5, samples are evaluated and samples with excess variation (usually due to excess variability in the read depth signal) are removed from further cnv discovery, but they are added back in for final genotyping. You can see the list of "discovery samples" in cnv_output/cnv_stage5/eval/DiscoverySamples.list. It will no doubt list these 40 samples. There is a pdf in there and some other files that can help you see the distribution and which samples are outliers.

  • SunhyeSunhye KoreaMember

    Thanks Bob.
    The question of the number of samples was resolved.
    Then, How to resolve the problem about CNV_Stage7/seq4?
    I want to finish CNVDiscoveryPipeline.q perfectly.

  • SunhyeSunhye KoreaMember

    Hi Bob.
    Thank you for your efforts.
    I attmpt to run using r1602.
    But I occur error in CNVStage2.

    ERROR 14:27:42,701 FunctionEdge - Error:  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/BiO/psh/Project/sv/tmpdir'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/BiO/psh/tools/svtoolkit/lib/SVToolkit.jar:/BiO/psh/tools/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/BiO/psh/tools/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.apps.MergeGenotyperOutput'  '-O' '/BiO/psh/Project/sv/r1602/cnv_stage2/seq_21/seq_21.genotypes.unfiltered.vcf.gz'  '-R' '/BiO/psh/tools/svtoolkit_2.00.1563/svtoolkit/bundle/reference_metadata_bundles/1000G_phase1/human_g1k_v37.fasta'  '-runDirectory' 'r1602/cnv_stage2/seq_21'  '-runFilePrefix' 'seq_21'  
    ERROR 14:27:42,712 FunctionEdge - Contents of /BiO/psh/Project/sv/r1602/cnv_stage2/seq_21/logs/CNVDiscoveryStage2-61.out:
    Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sv/apps/MergeGenotyperOutput : Unsupported major.minor version 51.0
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
        at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
    Could not find the main class: org.broadinstitute.sv.apps.MergeGenotyperOutput.  Program will exit. 
    INFO  14:27:42,714 QGraph - Writing incremental jobs reports... 
    INFO  14:27:42,715 QGraph - 7 Pend, 0 Run, 1 Fail, 60 Done 
    INFO  14:27:42,719 QCommandLine - Writing final jobs report... 
    INFO  14:27:42,719 QCommandLine - Done with errors
    

    I used the previous SVPreprocessing data created by r1592.
    My java version is 1.7.0_80.
    Does the problem occur because the svtoolkit version don't match between SVPreprocessing.q and CNVDiscoveryPipeline.q ?
    Otherwise, the Java version is the problem?

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    That error means you are not running java 7 in the recursive Queue invocations.

  • SunhyeSunhye KoreaMember

    Hi bob .
    My system's java is 1.7.0_80.

    [email protected]:~$ /usr/lib/jvm/java-7-oracle/jre/bin/java -version
    java version "1.7.0_80"
    Java(TM) SE Runtime Environment (build 1.7.0_80-b15)
    Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)
    

    Previously, though the same method and java version was used, this problem doesn't occur.
    So, I attempt to change java version such as java-8-oracle and java-7-openjdk-amd64,however, this problem continuously occur.

    I use SGE. and SGE's Path enviroment is

    sge_o_path: /BiO/psh/tools/svtoolkit/bwa:/usr/lib/jvm/java-7-oracle/bin:/BiO/psh/tools/samtools-1.1/bin:/BiO/psh/tools/bwa:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/bin/FastQC:/BiO/BioTools/plink-1.07-x86_64:/BiO/ycparkworking/mongodb/mongodb-linux-x86_64-3.0.3/bin:/usr/lib/jvm/java-7-oracle/bin:/usr/lib/jvm/java-7-oracle/db/bin:/usr/lib/jvm/java-7-oracle/jre/bin:/usr/lib/jvm/java-7-oracle/jre/bin

    I don't know why this problem suddenly happens.
    Do you know how to solve this problem?

  • SunhyeSunhye KoreaMember

    Thanks Bob!
    I solved this problem !
    And I run CNVDiscoveryPipeline.q using r1602 and I finally ended up the CNV Discovery successfully.
    Thank you for your efforts sincerely.

  • bhandsakerbhandsaker Member, Broadie, Moderator admin

    Great! It would be nice if you described what the underlying problem turned out to be, so that it might help others.

  • SunhyeSunhye KoreaMember
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