java.lang.IllegalArgumentException: the 'to' index must be between 'from' and the length of the data/position sequence

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via GitHub by asmirnov239
, 1 year ago
the 'to' index must be between 'from' and the length of the data/position sequence
via GitHub by achevali
, 6 months ago
There must be at least one contig above the threshold length in the sequence dictionary.
java.lang.IllegalArgumentException: the 'to' index must be between 'from' and the length of the data/position sequence
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:609)
at org.broadinstitute.hellbender.utils.param.ParamUtils.inRange(ParamUtils.java:80)
at org.broadinstitute.hellbender.utils.hmm.ForwardBackwardAlgorithm$Result.logProbability(ForwardBackwardAlgorithm.java:141)
at org.broadinstitute.hellbender.tools.exome.germlinehmm.GenotypeCopyNumberTriStateSegments.lambda$calculateLog10GP$6(GenotypeCopyNumberTriStateSegments.java:197)
at java.util.stream.ReferencePipeline$6$1.accept(ReferencePipeline.java:244)
at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:545)
at java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:260)
at java.util.stream.DoublePipeline.toArray(DoublePipeline.java:506)
at org.broadinstitute.hellbender.tools.exome.germlinehmm.GenotypeCopyNumberTriStateSegments.calculateLog10GP(GenotypeCopyNumberTriStateSegments.java:198)
at org.broadinstitute.hellbender.tools.exome.germlinehmm.GenotypeCopyNumberTriStateSegments.lambda$composeVariantContext$0(GenotypeCopyNumberTriStateSegments.java:125)
at java.util.stream.IntPipeline$4$1.accept(IntPipeline.java:250)
at java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:110)
at java.util.Spliterator$OfInt.forEachRemaining(Spliterator.java:693)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at org.broadinstitute.hellbender.tools.exome.germlinehmm.GenotypeCopyNumberTriStateSegments.composeVariantContext(GenotypeCopyNumberTriStateSegments.java:141)
at org.broadinstitute.hellbender.tools.exome.germlinehmm.GenotypeCopyNumberTriStateSegments.makeCalls(GenotypeCopyNumberTriStateSegments.java:104)
at org.broadinstitute.hellbender.tools.exome.germlinehmm.CopyNumberTriStateSegmentCaller.doWork(CopyNumberTriStateSegmentCaller.java:121)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:108)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:166)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)

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