java.lang.IllegalStateException

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

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  • The original PLs do not have enough values; accessing index 10000 but size is 10000
  • The original PLs do not have enough values; accessing index 10000 but size is 10000
  • The original PLs do not have enough values; accessing index 10000 but size is 10000
  • Stack trace

    • java.lang.IllegalStateException: The original PLs do not have enough values; accessing index 10000 but size is 10000 at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.generatePLs(GATKVariantContextUtils.java:1637) at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.mergeRefConfidenceGenotypes(GATKVariantContextUtils.java:1553) at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.referenceConfidenceMerge(GATKVariantContextUtils.java:1124) at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:191) at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:112) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)

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