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via broadinstitute.org by Unknown author, 1 year ago
via broadinstitute.org by Unknown author, 1 year ago
via broadinstitute.org by Unknown author, 1 year ago
java.lang.ArrayIndexOutOfBoundsException: 10000	at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.generatePL(ReferenceConfidenceVariantContextMerger.java:357)	at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.mergeRefConfidenceGenotypes(ReferenceConfidenceVariantContextMerger.java:331)	at org.broadinstitute.gatk.utils.variant.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:134)	at org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.endPreviousStates(CombineGVCFs.java:265)	at org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.reduce(CombineGVCFs.java:189)	at org.broadinstitute.gatk.tools.walkers.variantutils.CombineGVCFs.reduce(CombineGVCFs.java:110)	at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:291)	at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:280)	at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:279)	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:319)	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)