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Crash in unifiedgenotyper

sasignorsasignor University of Southern CaliforniaMember

Command:
/jre1.7.0/bin/java -Xmx80g -jar /next-gen_example_sim/bin/GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar \
-T UnifiedGenotyper \
-out_mode EMIT_ALL_CONFIDENT_SITES \
-glm SNP \
-R $REF_PFX \
-nt 16 \
followed by ~186 input bam files.

Error:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 96
at org.broadinstitute.sting.gatk.walkers.genotyper.DiploidSNPGenotypeLikelihoods.getCache(DiploidSNPGenotypeLikelihoods.java:298)
at org.broadinstitute.sting.gatk.walkers.genotyper.DiploidSNPGenotypeLikelihoods.inCache(DiploidSNPGenotypeLikelihoods.java:262)
at org.broadinstitute.sting.gatk.walkers.genotyper.DiploidSNPGenotypeLikelihoods.add(DiploidSNPGenotypeLikelihoods.java:229)
at org.broadinstitute.sting.gatk.walkers.genotyper.DiploidSNPGenotypeLikelihoods.add(DiploidSNPGenotypeLikelihoods.java:190)
at org.broadinstitute.sting.gatk.walkers.genotyper.DiploidSNPGenotypeLikelihoods.add(DiploidSNPGenotypeLikelihoods.java:176)
at org.broadinstitute.sting.gatk.walkers.genotyper.SNPGenotypeLikelihoodsCalculationModel.getLikelihoods(SNPGenotypeLikelihoodsCalculationModel.java:114)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoods(UnifiedGenotyperEngine.java:331)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:232)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:367)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:143)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:98)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8):
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: 96

I found this documented somewhat for Haplotype caller, but the solution didn't look applicable here. These are pooled samples so we must use unified genotyper.

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @sasignor‌

    Hi,

    Can you try running this without the -nt 16? Users have reported issues with it.

    Thanks,
    Sheila

  • sasignorsasignor University of Southern CaliforniaMember

    I'll mention that it worked fine with the -nt 16 for this same script minus about 7 of the input files. The additional input files required conversion from an older quality format and the --filter_mismatching_base_and_quals tag during formation of the bam files.

    Those are the only variables that changed between a script that worked and a script that had this error.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @sasignor Before we can go any further , we have to ask you to run this with the latest version and without any multithreading. I'm sorry but this is not optional.

  • sasignorsasignor University of Southern CaliforniaMember

    Will do. I will report back in a few days when it has had a chance to run.

  • sasignorsasignor University of Southern CaliforniaMember
    edited October 2014

    Ok, with the most recent version and not -nt 16 flag

    /home/jre1.7.0/bin/java -Xmx20g -jar /home/next-gen/bin/GenomeAnalysisTK.jar \
    -T UnifiedGenotyper \
    -out_mode EMIT_ALL_CONFIDENT_SITES \
    -glm SNP \
    -R $REF_PFX \

    The same error is being thrown.

    INFO 05:42:54,276 ProgressMeter - 3R:22008513 6.8126592E7 5.6 d 118.7 m 54.5% 10.3 d 4.7 d
    INFO 05:43:54,277 ProgressMeter - 3R:22017913 6.8126592E7 5.6 d 118.7 m 54.5% 10.3 d 4.7 d
    INFO 05:44:54,278 ProgressMeter - 3R:22026997 6.8142976E7 5.6 d 118.7 m 54.5% 10.3 d 4.7 d

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    java.lang.ArrayIndexOutOfBoundsException: 96
    at org.broadinstitute.gatk.tools.walkers.genotyper.DiploidSNPGenotypeLikelihoods.getCache(DiploidSNPGenotypeLikelihoods.java:298)
    at org.broadinstitute.gatk.tools.walkers.genotyper.DiploidSNPGenotypeLikelihoods.inCache(DiploidSNPGenotypeLikelihoods.java:262)
    at org.broadinstitute.gatk.tools.walkers.genotyper.DiploidSNPGenotypeLikelihoods.add(DiploidSNPGenotypeLikelihoods.java:229)
    at org.broadinstitute.gatk.tools.walkers.genotyper.DiploidSNPGenotypeLikelihoods.add(DiploidSNPGenotypeLikelihoods.java:190)
    at org.broadinstitute.gatk.tools.walkers.genotyper.DiploidSNPGenotypeLikelihoods.add(DiploidSNPGenotypeLikelihoods.java:176)
    at org.broadinstitute.gatk.tools.walkers.genotyper.SNPGenotypeLikelihoodsCalculationModel.getLikelihoods(SNPGenotypeLikelihoodsCalculationModel.java:115)
    at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateLikelihoods(UnifiedGenotypingEngine.java:305)
    at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotypingEngine.java:189)
    at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:367)
    at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:143)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
    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:314)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    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.engine.CommandLineGATK.main(CommandLineGATK.java:107)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
    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: 96
    ERROR ------------------------------------------------------------------------------------------
  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @sasignor‌

    Hi,

    Thanks. Can you submit a snippet of the file that is causing the error? Instructions on how to do so are here: http://gatkforums.broadinstitute.org/discussion/1894/how-do-i-submit-a-detailed-bug-report

    -Sheila

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