java.lang.RuntimeException

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

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Solutions on the web7568

  • java.lang.IllegalArgumentException: Comparison method violates its general contract!
  • via Atlassian JIRA by Oswaldo Hernandez [Atlassian] Bugmaster, 1 year ago
    java.lang.IllegalArgumentException: Comparison method violates its general contract!
  • via broadinstitute.org by Unknown author, 10 months ago
    java.lang.IllegalArgumentException: Comparison method violates its general contract!
  • Stack trace

    • java.lang.RuntimeException: java.lang.IllegalArgumentException: Comparison method violates its general contract! at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTectWalker.map(MuTectWalker.java:865) at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTectWalker.map(MuTectWalker.java:34) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:77) at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:61) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:225) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:104) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:227) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:89) Caused by: java.lang.IllegalArgumentException: Comparison method violates its general contract! at java.util.TimSort.mergeLo(TimSort.java:747) at java.util.TimSort.mergeAt(TimSort.java:483) at java.util.TimSort.mergeCollapse(TimSort.java:410) at java.util.TimSort.sort(TimSort.java:214) at java.util.TimSort.sort(TimSort.java:173) at java.util.Arrays.sort(Arrays.java:659) at java.util.Collections.sort(Collections.java:217) at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTectWalker.map(MuTectWalker.java:664) ... 8 more

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