50b aligned to Chr1A:536904672-536904820.
at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:140)
at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:210)
at htsjdk.samtools.AsyncSAMFileWriter.synchronouslyClose(AsyncSAMFileWriter.java:38)
at htsjdk.samtools.util.AbstractAsyncWriter.close(AbstractAsyncWriter.java:89)
at org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter.close(SAMFileGATKReadWriter.java:26)
at org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.closeTool(SplitNCigarReads.java:197)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1043)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Caused by: htsjdk.samtools.SAMException: Exception creating BAM index for record A00821:774:H5KM3DSX2:3:1628:6551:31281 1/2 150b aligned to Chr1A:536904672-536904820.
at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:119)
at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:137)
... 12 more
Caused by: java.lang.IllegalStateException: Read position too high for BAI bin indexing.
at htsjdk.samtools.SAMRecord.computeIndexingBin(SAMRecord.java:1577)
at htsjdk.samtools.BAMIndexer$BAMIndexBuilder$1.getIndexingBin(BAMIndexer.java:234)
at htsjdk.samtools.BinningIndexBuilder.processFeature(BinningIndexBuilder.java:83)
at htsjdk.samtools.BAMIndexer$BAMIndexBuilder.processAlignment(BAMIndexer.java:222)
at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:117)
