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UnifiedGenotyper: Stack Trace Error- ArrayIndexOutOfBoundsException

WaltLWaltL Member
edited October 2012 in Ask the GATK team

I received the error listed below, and was wondering if I could get some input. I dId not find similar error on Wiki for the UnifiedGenotyper.

When I run the script w/o the BED file, no error occurs, but the run will take > 30 days to traverse the genome, so I'm trying to limit the genomic regions for variant calling with the BED file. I've run dos2unix on BED, and checked to make sure there are no extraneous chars., newline, etc... it's clean.

Thanks for any suggestions you may have.

java -Djava.io.tmpdir=/dir/java.tmp -Xmx60g -jar /usr/local/gatk/GenomeAnalysisTK.jar -T UnifiedGenotyper -L Han.bed -R Han_GATK_idx/Han.fa -I BC8_reducedreads/BC8.reduced.bam -o BC8.UG -nt 6

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

java.lang.ArrayIndexOutOfBoundsException: 200
at org.broadinstitute.sting.gatk.contexts.ReferenceContext.getBase(ReferenceContext.java:180)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.getFilteredAndStratifiedContexts(UnifiedGenotyperEngine.java:524)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:185)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:354)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:119)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:65)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:70)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.1-11-g13c0244):
ERROR
ERROR Please visit the wiki 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: 200

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    Hi Walt, this sounds like an "off by one" error. You need to check the indexing of the intervals -- whether the start position is counted from 0 or 1. See the FAQ on input files for details on why this can be a problem with BED files.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    Hi Walt, this sounds like an "off by one" error. You need to check the indexing of the intervals -- whether the start position is counted from 0 or 1. See the FAQ on input files for details on why this can be a problem with BED files.

  • WaltLWaltL Member

    Thanks Geraldine. Problem solved!

  • chenyu600chenyu600 Member ✭✭

    Hi @Geraldine,
    I get the same problem with "MESSAGE: 200", and I confirmed that the bed file is meet the requirement, could you give me some suggestions.

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

    java.lang.ArrayIndexOutOfBoundsException: 200
    at org.broadinstitute.sting.gatk.contexts.ReferenceContext.getBase(ReferenceContext.java:180)
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.getFilteredAndStratifiedContexts(UnifiedGenotyperEngine.java:524)
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:185)
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:354)
    at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:119)
    at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:65)
    at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
    at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:70)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:619)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.1-8-g5efb575):
    ERROR
    ERROR Please visit the wiki 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: 200
    ERROR ------------------------------------------------------------------------------------------
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @chenyu600, I'm sorry but you're using an old version that is no longer supported. I can only help you if you find that this issue also occurs with the latest version of GATK.

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