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Function Edge-Error

jfarrelljfarrell Member ✭✭

When running the CNV pipeline (April 2015 release) , GenomeSTRiP is generating the following errors.

ERROR 23:55:26,355 FunctionEdge - Error:  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/restricted/projectnb/casa/sv/gs/.queue/tmp'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.gatk.queue.QCommandLine'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  '-S' '/restricted/projectnb/casa/sv/gs/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage8.q'  '-S' '/restricted/projectnb/casa/sv/gs/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q' '-S' '/restricted/projectnb/casa/sv/gs/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q'  '-S' '/restricted/projectnb/casa/sv/gs/svtoolkit/qscript/SVQScript.q'  '-gatk' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar'  '-jobLogDir' 'run.bi/cnv_stage8/seq_12/logs'  '-memLimit' '2.0'  '-jobRunner' 'GridEngine'  '-gatkJobRunner' 'GridEngine'  -run  '-sequenceName' '12'  '-runDirectory' 'run.bi/cnv_stage8/seq_12'  '-sentinelFile' 'run.bi/cnv_sentinel_files/stage_8_seq_12.sent'  --disableJobReport  '-configFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/conf/genstrip_parameters.txt'  '-R' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.fasta'  '-ploidyMapFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt'  '-genomeMaskFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.svmask.fasta' '-genomeMaskFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.lcmask.fasta'  '-copyNumberMaskFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.gcmask.fasta'  '-readDepthMaskFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.rdmask.bed'  '-genderMaskBedFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.gendermask.bed'  '-vdjBedFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.vdjregions.bed'  '-genderMapFile' 'adsp_gender.map'  '-md' 'run.bi/metadata'  -disableGATKTraversal  '-I' 'run.bi/cnv_stage6/seq_12/seq_12.merged_headers.bam'  '-vcf' 'run.bi/cnv_stage7/seq_12/seq_12.brig.sites.vcf'  '-genotypingParallelRecords' '1000'  '-duplicateScoreThreshold' '0.0'


and latter see this


ERROR 23:54:36,576 FunctionEdge - Error: ClassifySelectedVariants: List(/restricted/projectnb/casa/sv/gs/run.bi/cnv_stage8/seq_12/logs/SVGenotyper2) > List(/restricted/projectnb/casa/sv/gs/run.bi/cnv_stage8/seq_12/eval/SelectedVariants.classify.dat)
java.io.FileNotFoundException: run.bi/cnv_stage8/seq_12/eval/CopyNumberClass.report.dat (No such file or directory)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(FileInputStream.java:138)
        at scala.io.Source$.fromFile(Source.scala:90)
        at scala.io.Source$.fromFile(Source.scala:75)
        at org.broadinstitute.sv.discovery.cnv.CNVDiscoveryStageBase$ClassifySelectedVariants.run(CNVDiscoveryStageBase.q:55)
        at org.broadinstitute.gatk.queue.engine.InProcessRunner.start(InProcessRunner.scala:53)
        at org.broadinstitute.gatk.queue.engine.FunctionEdge.start(FunctionEdge.scala:84)
        at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:434)
        at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
        at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
        at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
        at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
INFO  23:54:36,578 QGraph - 2 Pend, 1 Run, 0 Fail, 1 Done
INFO  23:55:05,727 QGraph - Writing incremental jobs reports...
INFO  23:55:05,730 QGraph - 2 Pend, 0 Run, 1 Fail, 1 Done
INFO  23:55:05,732 QCommandLine - Writing final jobs report...
INFO  23:55:05,732 QCommandLine - Done with errors
INFO  23:55:05,733 QGraph - -------

When I rerun it I get this.....

lRecords' '1000'  '-duplicateScoreThreshold' '0.0'
INFO  09:47:23,314 FunctionEdge - Output written to /restricted/projectnb/casa/sv/gs/run.bi/logs/CNVDiscoveryPipeline-240.out
INFO  09:47:23,403 DrmaaJobRunner - Submitted job id: 8370150
INFO  09:47:23,403 QGraph - 44 Pend, 15 Run, 0 Fail, 185 Done

and the 15 tasks will eventually fail.

I have rerun this several times and have not be able to get beyond this step.

Tagged:

Best Answers

Answers

  • skashinskashin Member ✭✭

    Hi,

    There was a Queue dependency problem (that we recently fixed) that causes this behavior when the CNV pipeline is restarted.
    The easiest work-around is to look for the Stage8 chromosomes that failed - there will be .fail files in the cnv_sentinel_files subdirectory, e.g.
    cnv_output/cnv_sentinel_files/.stage_8_seq_12.sent.fail
    Then, for those chromosomes that failed, remove the entire output of Stage8, e.g.
    rm -rf cnv_output/cnv_stage8/seq_12/
    After that, restart the CNV pipeline

    Seva

  • jfarrelljfarrell Member ✭✭

    I followed the above steps and restarted the CNVPipeline run. One error then occurred among the 15 tasks restarted. The other 14 are still running (and hopefully will finish after the restart). There is a duplicate entry found in the dat file. Any solutions for this ERROR?

    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace
    java.lang.RuntimeException: Duplicate entries found in aux file run.bi/cnv_stage10/seq_9/seq_9.adjacent_merged.genotypes.gmm.dat: CNV_9_43471949_43483226
            at org.broadinstitute.sv.annotation.AuxFileReader.getInputLine(AuxFileReader.java:97)
            at org.broadinstitute.sv.annotation.ClusterSeparationAnnotator.calculateClusterSeparationStats(ClusterSeparationAnnotator.java:208)
            at org.broadinstitute.sv.annotation.ClusterSeparationAnnotator.annotate(ClusterSeparationAnnotator.java:150)
            at org.broadinstitute.sv.annotation.SVAnnotator.annotate(SVAnnotator.java:235)
            at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.annotateContext(SVVariantAnnotatorWalker.java:219)
            at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.processVCFFile(SVVariantAnnotatorWalker.java:167)
            at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.map(SVVariantAnnotatorWalker.java:121)
            at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.map(SVVariantAnnotatorWalker.java:71)
            at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:106)
            at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
            at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
            at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
            at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
            at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:125)
            at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
            at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
            at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:79)
            at org.broadinstitute.sv.main.SVAnnotator.main(SVAnnotator.java:92)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
    ##### ERROR
    ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
    ##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
    ##### ERROR Visit our website and forum for extensive documentation and answers to
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR MESSAGE: Duplicate entries found in aux file run.bi/cnv_stage10/seq_9/seq_9.adjacent_merged.genotypes.gmm.dat: CNV_9_43471949_43483226
    ##### ERROR ------------------------------------------------------------------------------------------
    INFO  10:19:05,050 QGraph - Writing incremental jobs reports...
    INFO  10:19:05,051 QGraph - 3 Pend, 0 Run, 1 Fail, 5 Done
    INFO  10:19:05,052 QCommandLine - Writing final jobs report...
    INFO  10:19:05,053 QCommandLine - Done with errors
    INFO  10:19:05,054 QGraph - -------
    INFO  10:19:05,055 QGraph - Failed:   'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/restricted/projectnb/casa/sv/gs/.queue/tmp'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.main.SVAnnotator'  '-O' '/restricted/projectnb/casa/sv/gs/run.bi/cnv_stage10/seq_9/seq_9.adjacent_merged.genotypes.annotated.vcf'  '-vcf' 'run.bi/cnv_stage10/seq_9/seq_9.adjacent_merged.genotypes.unfiltered.vcf'  '-R' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.fasta'  '-md' 'run.bi/metadata'  '-auxFilePrefix' 'run.bi/cnv_stage10/seq_9/seq_9.adjacent_merged.genotypes'  '-reportDirectory' 'run.bi/cnv_stage10/seq_9/eval'  '-genderMapFile' 'adsp_gender.map'  '-ploidyMapFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt' -A ClusterSeparation -A GCContent -A GenotypeLikelihoodStats -A NonVariant -A Redundancy -A CopyNumberClass -A CNQuality '-filterVariants' 'false'  '-writeReport' 'true'  '-writeSummary' 'true'  '-comparisonFile' 'run.bi/cnv_stage10/seq_9/seq_9.adjacent_merged.genotypes.unfiltered.vcf'  '-duplicateOverlapThreshold' '0.5'  '-duplicateScoreThreshold' '0.0'  '-A' 'BedFileOverlap'  '-bedFileTag' 'VDJ'  '-bedFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.vdjregions.bed'
    INFO  10:19:05,056 QGraph - Log:     /restricted/projectnb/casa/sv/gs/run.bi/cnv_stage10/seq_9/logs/SVGenotyper2-6.out
    INFO  10:19:05,056 QCommandLine - Script failed: 3 Pend, 0 Run, 1 Fail, 5 Done
    INFO  10:19:28,439 QGraph - Writing incremental jobs reports...
    INFO  10:19:28,440 QGraph - 2 Pend, 0 Run, 1 Fail, 0 Done
    INFO  10:19:28,441 QCommandLine - Writing final jobs report...
    INFO  10:19:28,442 QCommandLine - Done with errors
    INFO  10:19:28,443 QGraph - -------
    INFO  10:19:28,447 QGraph - Failed:   'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/restricted/projectnb/casa/sv/gs/.queue/tmp'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.gatk.queue.QCommandLine'  '-cp' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/Queue.jar'  '-S' '/restricted/projectnb/casa/sv/gs/svtoolkit/qscript/SVGenotyper2.q'  '-S' '/restricted/projectnb/casa/sv/gs/svtoolkit/qscript/SVQScript.q'  '-gatk' '/restricted/projectnb/casa/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar'  '-jobLogDir' 'run.bi/cnv_stage10/seq_9/logs'  '-memLimit' '2.0'  '-jobRunner' 'GridEngine'  '-gatkJobRunner' 'GridEngine'  -run  --disableJobReport  '-configFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/conf/genstrip_parameters.txt'  '-P' 'depth.readCountCacheIgnoreGenomeMask:true'  '-P' 'genotyping.modules:depth'  '-R' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.fasta'  '-genomeMaskFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.svmask.fasta' '-genomeMaskFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.lcmask.fasta'  '-ploidyMapFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt'  '-readDepthMaskFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.rdmask.bed'  '-genderMaskBedFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.gendermask.bed'  '-vdjBedFile' '/restricted/projectnb/casa/sv/gs/svtoolkit/Homo_sapiens_assembly19/Homo_sapiens_assembly19.vdjregions.bed'  '-genderMapFile' 'adsp_gender.map'  '-md' 'run.bi/metadata'  -disableGATKTraversal  '-vcf' 'run.bi/cnv_stage9/seq_9/seq_9.adjacent_merged.sites.vcf'  '-parallelRecords' '1000'  '-I' 'run.bi/bam_headers/merged_headers.bam'  '-O' 'run.bi/cnv_stage10/seq_9/seq_9.adjacent_merged.genotypes.vcf'  '-runDirectory' 'run.bi/cnv_stage10/seq_9'  '-duplicateScoreThreshold' '0.0'
    INFO  10:19:28,448 QGraph - Log:     /restricted/projectnb/casa/sv/gs/run.bi/cnv_stage10/seq_9/logs/CNVDiscoveryStage10-1.out
    INFO  10:19:28,448 QCommandLine - Script failed: 2 Pend, 0 Run, 1 Fail, 0 Done
    INFO  10:19:46,883 QGraph - Writing incremental jobs reports...
    INFO  10:19:46,884 QGraph - 44 Pend, 14 Run, 1 Fail, 185 Done
    
  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    This feels like file corruption, perhaps because two jobs got run at the same time generating the same output file?
    For example, if some job from a prior run had no finished and the run was restarted.

    I would suggest that after you let this run complete, you clean out this particular set of outputs (under cnv_stage10/seq_9) and then rerun.
    In general, Queue creates zero-length .xxx.done files, where xxx is the main output of the job being run.

  • jfarrelljfarrell Member ✭✭

    The cnv_stage10/seq_9 directory was deleted and then the CNVPipeline restarted but the same error was generated.

    There is one duplicate record in the dat file......

    cut -f1 run.bi/cnv_stage10/seq_9/seq_9.adjacent_merged.genotypes.gmm.dat|sort|uniq -c|awk '$1 ==2 {print $0}'
    2 CNV_9_43471949_43483226

    I cam going to delete one of them and restart the job to see if that gets by the error.

  • jfarrelljfarrell Member ✭✭

    This is what was in the dat file......

    There are two duplicates but also a 3rd record that starts at the same location....

    CNV_9_43471949_43483226 4599    4   -1498.7543389171929 0.04397913129742841,0.37857508002111834,0.5482124382225004,0.029233350458952874 0.0,0.8792174286402376,1.758434857280475,2.6376522859207125 1.5316949215719688,7.658474607859843,15.316949215719687,22.97542382357953
    CNV_9_43471949_43483226 4599    4   -1498.7543389171929 0.04397913129742841,0.37857508002111834,0.5482124382225004,0.029233350458952874 0.0,0.8792174286402376,1.758434857280475,2.6376522859207125 1.5316949215719688,7.658474607859843,15.316949215719687,22.97542382357953
    CNV_9_43471949_43477607 2699    4   -1266.3079710756701 0.05676855895195865,0.3668121270640416,0.5458450213293998,0.03057429265460003   0.0,0.8165416194520304,1.6330832389040608,2.449624858356091 0.31894433867977434,1.5947216933988717,3.1894433867977434,4.784165080196615
    
  • jfarrelljfarrell Member ✭✭

    To get around this error, both the 2nd and 3rd line above had to be deleted.

    Further along this error was generated. Same sites----here were two records for CNV_9_43471949_43483226 and CNV_9_43471949_43477607. I deleted the 2nd line and restarted.

    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace
    java.lang.RuntimeException: Duplicate entries found in aux file run.bi/cnv_stage10/seq_9/seq_9.adjacent_merged.genotypes.counts.dat: CNV_9_43471949_43483226
            at org.broadinstitute.sv.annotation.AuxFileReader.getInputLine(AuxFileReader.java:97)
            at org.broadinstitute.sv.annotation.ClusterSeparationAnnotator.calculateClusterSeparationStats(ClusterSeparationAnnotator.java:209)
            at org.broadinstitute.sv.annotation.ClusterSeparationAnnotator.annotate(ClusterSeparationAnnotator.java:150)
            at org.broadinstitute.sv.annotation.SVAnnotator.annotate(SVAnnotator.java:235)
            at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.annotateContext(SVVariantAnnotatorWalker.java:219)
            at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.processVCFFile(SVVariantAnnotatorWalker.java:167)
            at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.map(SVVariantAnnotatorWalker.java:121)
            at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.map(SVVariantAnnotatorWalker.java:71)
            at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:106)
            at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
            at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
            at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
            at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
            at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:125)
            at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
            at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
            at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:79)
            at org.broadinstitute.sv.main.SVAnnotator.main(SVAnnotator.java:92)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
    ##### ERROR
    ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
    ##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
    ##### ERROR Visit our website and forum for extensive documentation and answers to
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR MESSAGE: Duplicate entries found in aux file run.bi/cnv_stage10/seq_9/seq_9.adjacent_merged.genotypes.counts.dat: CNV_9_43471949_43483226
    

    This was followed by the similar error at
    run.bi/cnv_stage10/seq_9/seq_9.adjacent_merged.genotypes.expected.dat

    The 2nd and 3rd record was deleted and the run restarted...

  • jfarrelljfarrell Member ✭✭

    The pipeline still gets an error in a later stage pointing to the same sites after the restart with the deletions.

  • jfarrelljfarrell Member ✭✭

    Thanks.
    I deleted the duplicate in the stage9 seq vcf. I also had to delete the stage_10/seq_9 directory. Once that was done the pipeline finished fine.

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