CommandLineGATK.main() has thrown an ArrayIndexOutOfBoundsException

We found this prefix in 3 webpages.
MapChildren (3)Typical messages (1)TraceDetailed Map
  1. java.lang.ArrayIndexOutOfBoundsException
    1.   at org.broadinstitute.cga.tools.gatk.utils.CGAAlignmentUtils.mismatchesInRefWindow()
    2.   at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.filterReads()
    3.   at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map()
    4.   at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map()
    5.   at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply()
    6.   at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply()
    7.   at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded()
    8.   at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute()
    9.   at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse()
    10.   at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse()
    11.   at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse()
    12.   at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute()
    13.   at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute()
    14.   at org.broadinstitute.sting.gatk.CommandLineExecutable.execute()
    15.   at org.broadinstitute.sting.commandline.CommandLineProgram.start()
    16.   at org.broadinstitute.sting.commandline.CommandLineProgram.start()
    17.   at org.broadinstitute.sting.gatk.CommandLineGATK.main()
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  1. java.lang.ArrayIndexOutOfBoundsException: 83 running MuTect — GATK-Forum

    First:2 years ago
    Last:2 years ago
  2. java.lang.ArrayIndexOutOfBoundsException: 83 running MuTect - GATK-Forum

    First:3 years ago
    Last:3 years ago
  3. java.lang.ArrayIndexOutOfBoundsException: 83 running MuTect — GATK-Forum

    First:1 year ago
    Last:2 years ago
MessageNumber of crashes
833
  1. java.lang.ArrayIndexOutOfBoundsException
    1.   at org.broadinstitute.cga.tools.gatk.utils.CGAAlignmentUtils.mismatchesInRefWindow()
    2.   at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.filterReads()
    3.   at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map()
    4.   at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map()
    5.   at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply()
    6.   at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply()
    7.   at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded()
    8.   at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute()
    9.   at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse()
    10.   at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse()
    11.   at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse()
    12.   at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute()
    13.   at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute()
    14.   at org.broadinstitute.sting.gatk.CommandLineExecutable.execute()
    15.   at org.broadinstitute.sting.commandline.CommandLineProgram.start()
    16.   at org.broadinstitute.sting.commandline.CommandLineProgram.start()
    17.   at org.broadinstitute.sting.gatk.CommandLineGATK.main()
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