java.lang.ArrayIndexOutOfBoundsException: 200

broadinstitute.org | 8 months ago
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    broadinstitute.org | 1 year ago
    java.lang.ArrayIndexOutOfBoundsException: 200
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    broadinstitute.org | 6 months ago
    java.lang.ArrayIndexOutOfBoundsException: 200
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    broadinstitute.org | 8 months ago
    java.lang.ArrayIndexOutOfBoundsException: 200
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    broadinstitute.org | 8 months ago
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    ERROR stack trace java.lang.ArrayIndexOutOfBoundsException: -4 - GATK-Forum

    broadinstitute.org | 1 year ago
    java.lang.ArrayIndexOutOfBoundsException: -4

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    Root Cause Analysis

    1. java.lang.ArrayIndexOutOfBoundsException

      200

      at org.broadinstitute.gatk.utils.contexts.ReferenceContext.getBase()
    2. org.broadinstitute.gatk
      CommandLineGATK.main
      1. org.broadinstitute.gatk.utils.contexts.ReferenceContext.getBase(ReferenceContext.java:179)
      2. org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.getFilteredAndStratifiedContexts(UnifiedGenotypingEngine.java:434)
      3. org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotypingEngine.java:196)
      4. org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:376)
      5. org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:148)
      6. org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
      7. org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
      8. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
      9. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
      10. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
      11. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
      12. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
      13. org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
      14. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
      15. org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
      16. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
      17. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
      18. org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
      18 frames