java.lang.RuntimeException: java.lang.ArrayIndexOutOfBoundsException: 83

broadinstitute.org | 7 months ago
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    java.lang.ArrayIndexOutOfBoundsException: 83 running MuTect - GATK-Forum

    broadinstitute.org | 1 year ago
    java.lang.RuntimeException: java.lang.ArrayIndexOutOfBoundsException: 83
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    java.lang.ArrayIndexOutOfBoundsException: 83 running MuTect — GATK-Forum

    broadinstitute.org | 7 months ago
    java.lang.RuntimeException: java.lang.ArrayIndexOutOfBoundsException: 83
  3. 0

    java.lang.ArrayIndexOutOfBoundsException: 83 running MuTect — GATK-Forum

    broadinstitute.org | 1 month ago
    java.lang.RuntimeException: java.lang.ArrayIndexOutOfBoundsException: 83
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    Comparison method violates its general contract! - GATK-Forum

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    java.lang.RuntimeException: java.lang.IllegalArgumentException: Comparison method violates its general contract!
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    Comparison method violates its general contract! — GATK-Forum

    broadinstitute.org | 7 months ago
    java.lang.RuntimeException: java.lang.IllegalArgumentException: Comparison method violates its general contract!

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    Root Cause Analysis

    1. java.lang.ArrayIndexOutOfBoundsException

      83

      at org.broadinstitute.cga.tools.gatk.utils.CGAAlignmentUtils.mismatchesInRefWindow()
    2. org.broadinstitute.cga
      MuTect.map
      1. org.broadinstitute.cga.tools.gatk.utils.CGAAlignmentUtils.mismatchesInRefWindow(CGAAlignmentUtils.java:135)
      2. org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.filterReads(MuTect.java:787)
      3. org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:511)
      4. org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:79)
      4 frames
    3. org.broadinstitute.sting
      CommandLineGATK.main
      1. org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
      2. org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
      3. org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
      4. org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
      5. org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
      6. org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
      7. org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
      8. org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
      9. org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
      10. org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121)
      11. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
      12. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
      13. org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)
      13 frames