java.lang.ArrayIndexOutOfBoundsException: 10000

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    java.lang.ArrayIndexOutOfBoundsException: 10000
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    java.lang.ArrayIndexOutOfBoundsException: 10000
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    java.lang.ArrayIndexOutOfBoundsException: 10000
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    broadinstitute.org | 2 months ago
    java.lang.ArrayIndexOutOfBoundsException: 10000

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    Root Cause Analysis

    1. java.lang.ArrayIndexOutOfBoundsException

      10000

      at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.generatePL()
    2. org.broadinstitute.gatk
      CommandLineGATK.main
      1. org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.generatePL(ReferenceConfidenceVariantContextMerger.java:357)
      2. org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.mergeRefConfidenceGenotypes(ReferenceConfidenceVariantContextMerger.java:331)
      3. org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:134)
      4. org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.endPreviousStates(CombineGVCFs.java:265)
      5. org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.reduce(CombineGVCFs.java:189)
      6. org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.reduce(CombineGVCFs.java:110)
      7. org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:291)
      8. org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:280)
      9. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:279)
      10. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
      11. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
      12. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
      13. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
      14. org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
      15. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
      16. org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
      17. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
      18. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
      19. org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
      19 frames