java.lang.ArrayIndexOutOfBoundsException: 83 running MuTect

pkMyt1pkMyt1 Chapel Hill, NCMember

Hello. I am getting a java.lang.ArrayIndexOutOfBoundsException: 83 error when running MuTect. I got this error on v1.1.4 and built the latest version this morning (v1.1.7) but the error is still there. None of the posts about this error apply to me. It appears to be the same position always in the BAM file but I cannot determine what is wrong or how to get past it. The analysis looks like it gets through chromosomes 1, 2, and most of 3 before the crash. I have tried running using commands to ignore the error but that doesn't help. If you could point me in a direction to solve this I would be very greatful. The stack trace is pasted below.

Error processing chr3:195505766
java.lang.ArrayIndexOutOfBoundsException: 83
at org.broadinstitute.cga.tools.gatk.utils.CGAAlignmentUtils.mismatchesInRefWindow(CGAAlignmentUtils.java:135)
at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.filterReads(MuTect.java:787)
at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:511)
at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:79)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.RuntimeException: java.lang.ArrayIndexOutOfBoundsException: 83
at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:649)
at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:79)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 83
at org.broadinstitute.cga.tools.gatk.utils.CGAAlignmentUtils.mismatchesInRefWindow(CGAAlignmentUtils.java:135)
at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.filterReads(MuTect.java:787)
at org.broadinstitute.cga.tools.gatk.walkers.cancer.mutect.MuTect.map(MuTect.java:511)
... 14 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.1-0-g72492bb):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: java.lang.ArrayIndexOutOfBoundsException: 83
ERROR ------------------------------------------------------------------------------------------

[pkMyt1@CLASPIN-1 GATK]$

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Answers

  • nriddifordnriddiford ParisMember

    I have the same problem - did you manage to fix this?

  • shleeshlee CambridgeMember, Broadie, Moderator

    Please follow the directions in left panel under Did you remember to?.

    1. Search using the upper-right search box, e.g. using the error message.
    2. Try the latest version of tools.
    3. Include tool and Java versions.
    4. Tell us whether you are following GATK Best Practices.
    5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
    6. For tool errors, include the error stacktrace as well as the exact command.
    7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
    8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
    9. For a seeming variant that is uncalled, include results of following Article#1235.
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