java.lang.ArrayIndexOutOfBoundsException: 97

broadinstitute.org | 6 months ago
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    HaplotypeCaller : stack trace java.lang.ArrayIndexOutOfBoundsException: 97 — GATK-Forum

    broadinstitute.org | 6 months ago
    java.lang.ArrayIndexOutOfBoundsException: 97
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    Root Cause Analysis

    1. java.lang.ArrayIndexOutOfBoundsException

      97

      at org.broadinstitute.sting.utils.fragments.FragmentUtils.mergeOverlappingPairedFragments()
    2. org.broadinstitute.sting
      CommandLineGATK.main
      1. org.broadinstitute.sting.utils.fragments.FragmentUtils.mergeOverlappingPairedFragments(FragmentUtils.java:256)
      2. org.broadinstitute.sting.utils.fragments.FragmentUtils.mergeOverlappingPairedFragments(FragmentUtils.java:200)
      3. org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.finalizeActiveRegion(HaplotypeCaller.java:814)
      4. org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.assembleReads(HaplotypeCaller.java:636)
      5. org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:564)
      6. org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:135)
      7. org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:564)
      8. org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:521)
      9. org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:251)
      10. org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:70)
      11. org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:100)
      12. org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286)
      13. org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
      14. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
      15. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
      16. org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
      16 frames