00:32:48.224 INFO HaplotypeCaller – Shutting down engine
[September 17, 2021 12:32:48 AM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=2398617600
java.nio.BufferUnderflowException
at java.nio.ByteBuffer.get(ByteBuffer.java:688)
at java.nio.DirectByteBuffer.get(DirectByteBuffer.java:285)
at java.nio.ByteBuffer.get(ByteBuffer.java:715)
at htsjdk.samtools.MemoryMappedFileBuffer.readBytes(MemoryMappedFileBuffer.java:34)
at htsjdk.samtools.AbstractBAMFileIndex.readBytes(AbstractBAMFileIndex.java:428)
at htsjdk.samtools.AbstractBAMFileIndex.verifyIndexMagicNumber(AbstractBAMFileIndex.java:376)
at htsjdk.samtools.AbstractBAMFileIndex.<init>(AbstractBAMFileIndex.java:70)
at htsjdk.samtools.AbstractBAMFileIndex.<init>(AbstractBAMFileIndex.java:64)
at htsjdk.samtools.CachingBAMFileIndex.<init>(CachingBAMFileIndex.java:56)
at htsjdk.samtools.BAMFileReader.getIndex(BAMFileReader.java:418)
at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:952)
at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:612)
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:533)
at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:405)
at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.loadNextIterator(SamReaderQueryingIterator.java:125)
at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.<init>(SamReaderQueryingIterator.java:66)
at org.broadinstitute.hellbender.engine.ReadsDataSource.prepareIteratorsForTraversal(ReadsDataSource.java:404)
at org.broadinstitute.hellbender.engine.ReadsDataSource.iterator(ReadsDataSource.java:330)
at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.iterator(MultiIntervalLocalReadShard.java:134)
at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.<init>(AssemblyRegionIterator.java:109)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:296)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:281)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039)
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)
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