java.lang.IllegalStateException: The original PLs do not have enough values; accessing index 10011 but size is 10000

broadinstitute.org | 5 days ago
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  1. 0

    BUG: java.lang.IllegalStateException: The original PLs do not have enough values — GATK-Forum

    broadinstitute.org | 3 months ago
    java.lang.IllegalStateException: The original PLs do not have enough values; accessing index 10000 but size is 10000
  2. 0

    BUG: java.lang.IllegalStateException: The original PLs do not have enough values — GATK-Forum

    broadinstitute.org | 5 days ago
    java.lang.IllegalStateException: The original PLs do not have enough values; accessing index 10000 but size is 10000
  3. 0

    BUG: java.lang.IllegalStateException: The original PLs do not have enough values - GATK-Forum

    broadinstitute.org | 2 years ago
    java.lang.IllegalStateException: The original PLs do not have enough values; accessing index 10000 but size is 10000
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    Root Cause Analysis

    1. java.lang.IllegalStateException

      The original PLs do not have enough values; accessing index 10011 but size is 10000

      at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.generatePLs()
    2. org.broadinstitute.gatk
      CommandLineGATK.main
      1. org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.generatePLs(GATKVariantContextUtils.java:1637)
      2. org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.mergeRefConfidenceGenotypes(GATKVariantContextUtils.java:1553)
      3. org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.referenceConfidenceMerge(GATKVariantContextUtils.java:1124)
      4. org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:191)
      5. org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:112)
      6. org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
      7. org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
      8. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
      9. org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
      10. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
      11. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
      12. org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
      13. org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
      14. org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
      15. org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
      16. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
      17. org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
      18. org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
      18 frames