java.lang.IllegalArgumentException

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    • java.lang.IllegalArgumentException at java.nio.ByteBuffer.allocate(ByteBuffer.java:330) at htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:195) at org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:329) at org.broadinstitute.gatk.tools.walkers.rnaseq.OverhangFixingManager$Splice.initialize(OverhangFixingManager.java:365) at org.broadinstitute.gatk.tools.walkers.rnaseq.OverhangFixingManager.addSplicePosition(OverhangFixingManager.java:171) at org.broadinstitute.gatk.tools.walkers.rnaseq.SplitNCigarReads.splitReadBasedOnCigar(SplitNCigarReads.java:280) at org.broadinstitute.gatk.tools.walkers.rnaseq.SplitNCigarReads.splitNCigarRead(SplitNCigarReads.java:233) at org.broadinstitute.gatk.tools.walkers.rnaseq.SplitNCigarReads.reduce(SplitNCigarReads.java:210) at org.broadinstitute.gatk.tools.walkers.rnaseq.SplitNCigarReads.reduce(SplitNCigarReads.java:118) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:251) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:240) 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.TraverseReadsNano.traverse(TraverseReadsNano.java:102) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315) 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:106)

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