java.lang.RuntimeException: java.lang.IllegalArgumentException: Comparison method violates its general contract!

broadinstitute.org | 4 weeks ago
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  1. 0

    Bug report: java.lang.IllegalArgumentException: Comparison method violates its general contract! - GATK-Forum

    broadinstitute.org | 2 years ago
    java.lang.RuntimeException: java.lang.IllegalArgumentException: Comparison method violates its general contract!
  2. 0

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

    broadinstitute.org | 4 weeks ago
    java.lang.IllegalArgumentException: Comparison method violates its general contract!
  3. 0

    Comparison method violates its general contract! — GATK-Forum

    broadinstitute.org | 8 months ago
    java.lang.IllegalArgumentException: Comparison method violates its general contract!
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  5. 0

    Comparison method violates its general contract! - GATK-Forum

    broadinstitute.org | 1 year ago
    java.lang.IllegalArgumentException: Comparison method violates its general contract!
  6. 0

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

    broadinstitute.org | 4 months ago
    java.lang.IllegalArgumentException: Comparison method violates its general contract!

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    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Comparison method violates its general contract!

      at java.util.TimSort.mergeLo()
    2. Java RT
      Collections.sort
      1. java.util.TimSort.mergeLo(TimSort.java:747)
      2. java.util.TimSort.mergeAt(TimSort.java:483)
      3. java.util.TimSort.mergeForceCollapse(TimSort.java:426)
      4. java.util.TimSort.sort(TimSort.java:223)
      5. java.util.TimSort.sort(TimSort.java:173)
      6. java.util.Arrays.sort(Arrays.java:659)
      7. java.util.Collections.sort(Collections.java:217)
      7 frames
    3. org.broadinstitute.cga
      MuTect.map
      1. org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:480)
      2. org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:34)
      2 frames
    4. org.broadinstitute.sting
      CommandLineGATK.main
      1. org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:243)
      2. org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:231)
      3. org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:287)
      4. org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:252)
      5. org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:120)
      6. org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:67)
      7. org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:23)
      8. org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:74)
      9. org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
      10. org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
      11. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
      12. org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
      13. org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
      13 frames