java.lang.IndexOutOfBoundsException: Index: 28, Size: 6

broadinstitute.org | 3 months ago
  1. 0

    IndexOutOfBoundsException in HaplotypeCaller (GATK 3.2) - GATK-Forum

    broadinstitute.org | 12 months ago
    java.lang.IndexOutOfBoundsException: Index: 28, Size: 6
  2. 0

    IndexOutOfBoundsException in HaplotypeCaller (GATK 3.2) — GATK-Forum

    broadinstitute.org | 4 months ago
    java.lang.IndexOutOfBoundsException: Index: 28, Size: 6
  3. 0

    IndexOutOfBoundsException in HaplotypeCaller (GATK 3.2) — GATK-Forum

    broadinstitute.org | 6 days ago
    java.lang.IndexOutOfBoundsException: Index: 28, Size: 6
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  5. 0

    IndexOutOfBoundsException in HaplotypeCaller (GATK 3.2) — GATK-Forum

    broadinstitute.org | 3 months ago
    java.lang.IndexOutOfBoundsException: Index: 28, Size: 6
  6. 0

    Running piper on M.Kaller_14_06

    GitHub | 2 years ago | vezzi
    java.lang.IndexOutOfBoundsException: Index: 28, Size: 6

  1. tyson925 4 times, last 6 months ago
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Root Cause Analysis

  1. java.lang.IndexOutOfBoundsException

    Index: 28, Size: 6

    at java.util.LinkedList.checkElementIndex()
  2. Java RT
    LinkedList.get
    1. java.util.LinkedList.checkElementIndex(Unknown Source)
    2. java.util.LinkedList.get(Unknown Source)
    2 frames
  3. org.broadinstitute.gatk
    CommandLineProgram.start
    1. org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraph.mergeDanglingTail(DanglingChainMergingGraph.java:272)
    2. org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraph.recoverDanglingTail(DanglingChainMergingGraph.java:184)
    3. org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraph.recoverDanglingTails(DanglingChainMergingGraph.java:131)
    4. org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.createGraph(ReadThreadingAssembler.java:202)
    5. org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.assemble(ReadThreadingAssembler.java:114)
    6. org.broadinstitute.gatk.tools.walkers.haplotypecaller.LocalAssemblyEngine.runLocalAssembly(LocalAssemblyEngine.java:164)
    7. org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.assembleReads(HaplotypeCaller.java:1022)
    8. org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:882)
    9. org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:218)
    10. org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708)
    11. org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704)
    12. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
    13. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    14. org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:273)
    15. org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
    16. org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
    17. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
    18. org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    19. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    20. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    20 frames