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)