java.lang.IndexOutOfBoundsException: Index: 32, Size: 32

broadinstitute.org | 3 months ago
  1. 0

    IndexOutOfBoundsException in HaplotypeCaller (GATK 3.2) - GATK-Forum

    broadinstitute.org | 1 year ago
    java.lang.IndexOutOfBoundsException: Index: 32, Size: 32
  2. 0

    IndexOutOfBoundsException in HaplotypeCaller (GATK 3.2) — GATK-Forum

    broadinstitute.org | 4 months ago
    java.lang.IndexOutOfBoundsException: Index: 32, Size: 32
  3. 0

    IndexOutOfBoundsException in HaplotypeCaller (GATK 3.2) — GATK-Forum

    broadinstitute.org | 1 week ago
    java.lang.IndexOutOfBoundsException: Index: 32, Size: 32
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  5. 0

    IndexOutOfBoundsException in HaplotypeCaller (GATK 3.2) — GATK-Forum

    broadinstitute.org | 3 months ago
    java.lang.IndexOutOfBoundsException: Index: 32, Size: 32
  6. 0

    [Weka] IndexOutOfBoundsException when obtaining folds

    GitHub | 2 years ago | DraXus
    java.lang.IndexOutOfBoundsException: Index: 107, Size: 107 java.util.ArrayList.rangeCheck(ArrayList.java:635) java.util.ArrayList.get(ArrayList.java:411) weka.core.Instances.instance(Instances.java:768) org.openml.weka.experiment.TaskResultProducer.doRun(TaskResultProducer.java:248) org.openml.weka.experiment.TaskBasedExperiment.nextIteration(TaskBasedExperiment.java:173) org.openml.weka.gui.OpenmlRunPanel$ExperimentRunner.run(OpenmlRunPanel.java:197)

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Root Cause Analysis

  1. java.lang.IndexOutOfBoundsException

    Index: 32, Size: 32

    at java.util.ArrayList.rangeCheck()
  2. Java RT
    ArrayList.get
    1. java.util.ArrayList.rangeCheck(ArrayList.java:635)
    2. java.util.ArrayList.get(ArrayList.java:411)
    2 frames
  3. org.broadinstitute.gatk
    NanoScheduler$ReadMapReduceJob.run
    1. org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraph.mergeDanglingTail(DanglingChainMergingGraph.java:272)
    2. org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraph.recoverDanglingTail(DanglingChainMergingGraph.java:184)
    3. org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.DanglingChainMergingGraph.recoverDanglingTails(DanglingChainMergingGraph.java:131)
    4. org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.createGraph(ReadThreadingAssembler.java:202)
    5. org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.assemble(ReadThreadingAssembler.java:114)
    6. org.broadinstitute.gatk.tools.walkers.haplotypecaller.LocalAssemblyEngine.runLocalAssembly(LocalAssemblyEngine.java:164)
    7. org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.assembleReads(HaplotypeCaller.java:1022)
    8. org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:882)
    9. org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:218)
    10. org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708)
    11. org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704)
    12. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
    12 frames
  4. Java RT
    Thread.run
    1. java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    2. java.util.concurrent.FutureTask.run(FutureTask.java:262)
    3. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    4. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    5. java.lang.Thread.run(Thread.java:745)
    5 frames