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

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  • Why muTect Error?
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    • java.lang.RuntimeException: java.lang.IllegalArgumentException: Comparison method violates its general contract! at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:712) at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:34) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:243) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:231) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:287) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:252) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:120) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:67) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:23) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:74) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93) 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.mergeForceCollapse(TimSort.java:426) at java.util.TimSort.sort(TimSort.java:223) 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.MuTect.map(MuTect.java:480) ... 14 more

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