error in UnifiedGenotyper

Dear GATK team, I am encountering the following error when running UnifiedGenotyper on the LSF cluster. This error is not consistent and occurs in ~5% of the jobs. When I pick the jobs that failed and re-run them with the same command and input files, they successfully go through. I will greatly appreciate your help.

java -Xmx10g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R reference.fa -glm BOTH -o out.vcf -nct 2 -I input.bam

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

java.lang.NullPointerException
at java.lang.String.checkBounds(Unknown Source)
at java.lang.String.(Unknown Source)
at net.sf.samtools.util.StringUtil.bytesToString(StringUtil.java:301)
at net.sf.samtools.BAMRecord.decodeReadName(BAMRecord.java:331)
at net.sf.samtools.BAMRecord.getReadName(BAMRecord.java:220)
at net.sf.samtools.BAMRecord.eagerDecode(BAMRecord.java:112)
at net.sf.samtools.SAMRecord.hashCode(SAMRecord.java:1489)
at org.broadinstitute.sting.utils.sam.GATKSAMRecord.hashCode(GATKSAMRecord.java:239)
at java.util.HashMap.hash(Unknown Source)
at java.util.HashMap.getEntry(Unknown Source)
at java.util.HashMap.containsKey(Unknown Source)
at org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap.containsPileupElement(PerReadAlleleLikelihoodMap.java:158)
at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.computeGeneralReadHaplotypeLikelihoods(PairHMMIndelErrorModel.java:296)
at org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel.computeDiploidReadHaplotypeLikelihoods(PairHMMIndelErrorModel.java:251)
at org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel.getLikelihoods(IndelGenotypeLikelihoodsCalculationModel.java:149)
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$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
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 2.8-1-g932cd3a):
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: Code exception (see stack trace for error itself)

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @ArtemPankin‌

    Hello,

    I see you are using an older version. Please upgrade to the latest version and try again, as this seems like a bug that has been fixed.

    If the latest version does not work, please try your command without the -nct argument.

    Also, you can use Queue to manage the jobs; it will retry failed jobs and save you time and tedious baby-sitting of the cluster jobs.

    -Sheila

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