java.lang.ArrayIndexOutOfBoundsException: -4

broadinstitute.org | 2 months ago
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    BaseRecalibrator: Array length mismatch detected. Malformed read — GATK-Forum

    broadinstitute.org | 2 months ago
    java.lang.ArrayIndexOutOfBoundsException: -4
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    BaseRecalibrator Error - GATK-Forum

    broadinstitute.org | 1 year ago
    java.lang.ArrayIndexOutOfBoundsException: -4
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    Halloween Easter Egg Bug

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    java.lang.ArrayIndexOutOfBoundsException: 4
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    Bitap pattern matching fails for sequences with N's

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    java.lang.ArrayIndexOutOfBoundsException: 4

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    Root Cause Analysis

    1. java.lang.ArrayIndexOutOfBoundsException

      -4

      at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon()
    2. org.broadinstitute.sting
      NanoScheduler$MapReduceJob.run
      1. org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158)
      2. org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246)
      3. org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542)
      4. org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595)
      5. org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530)
      6. org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663)
      7. org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428)
      8. org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243)
      9. org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)
      10. org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)
      11. org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
      12. org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$MapReduceJob.run(NanoScheduler.java:468)
      12 frames
    3. Java RT
      Thread.run
      1. java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
      2. java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
      3. java.util.concurrent.FutureTask.run(FutureTask.java:166)
      4. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
      5. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
      6. java.lang.Thread.run(Thread.java:679)
      6 frames