ProgressMeter - chr8:143589342 47.5 179990 3785.9 20:16:30.694 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 1.7017637300000001 20:16:30.695 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 252.08564849700002 20:16:30.695 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 119.95 sec 20:16:30.753 INFO HaplotypeCaller - Shutting down engine [2021年12月22日 20:16:30 JST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 47.76 minutes. Runtime.totalMemory()=826277888 java.nio.BufferUnderflowException at java.base/java.nio.Buffer.nextGetIndex(Buffer.java:707) at java.base/java.nio.DirectByteBuffer.getInt(DirectByteBuffer.java:684) at htsjdk.samtools.MemoryMappedFileBuffer.readInteger(MemoryMappedFileBuffer.java:39) at htsjdk.samtools.AbstractBAMFileIndex.readInteger(AbstractBAMFileIndex.java:443) at htsjdk.samtools.AbstractBAMFileIndex.query(AbstractBAMFileIndex.java:272) at htsjdk.samtools.CachingBAMFileIndex.getQueryResults(CachingBAMFileIndex.java:159) at htsjdk.samtools.CachingBAMFileIndex.getSpanOverlapping(CachingBAMFileIndex.java:70) at htsjdk.samtools.BAMFileReader.getFileSpan(BAMFileReader.java:914) at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:931) at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:612) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:550) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:417) at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.loadNextIterator(SamReaderQueryingIterator.java:130) at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.<init>(SamReaderQueryingIterator.java:69) at org.broadinstitute.hellbender.engine.ReadsPathDataSource.prepareIteratorsForTraversal(ReadsPathDataSource.java:412) at org.broadinstitute.hellbender.engine.ReadsPathDataSource.iterator(ReadsPathDataSource.java:336) at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.iterator(MultiIntervalLocalReadShard.java:134) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.<init>(AssemblyRegionIterator.java:86) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:188) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289)
72ページの「./120_run-HaplotyppeCaller.sh」で８番染色体の途中らへんで毎回エラーが起きます。 ググってもわからないのでわかる方教えていただけませんか！？
ProgressMeter - chr8:143589342 47.5 179990 3785.9 20:16:30.694 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 1.7017637300000001 20:16:30.695 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 252.08564849700002 20:16:30.695 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 119.95 sec 20:16:30.753 INFO HaplotypeCaller - Shutting down engine [2021年12月22日 20:16:30 JST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 47.76 minutes. Runtime.totalMemory()=826277888 java.nio.BufferUnderflowException at java.base/java.nio.Buffer.nextGetIndex(Buffer.java:707) at java.base/java.nio.DirectByteBuffer.getInt(DirectByteBuffer.java:684) at htsjdk.samtools.MemoryMappedFileBuffer.readInteger(MemoryMappedFileBuffer.java:39) at htsjdk.samtools.AbstractBAMFileIndex.readInteger(AbstractBAMFileIndex.java:443) at htsjdk.samtools.AbstractBAMFileIndex.query(AbstractBAMFileIndex.java:272) at htsjdk.samtools.CachingBAMFileIndex.getQueryResults(CachingBAMFileIndex.java:159) at htsjdk.samtools.CachingBAMFileIndex.getSpanOverlapping(CachingBAMFileIndex.java:70) at htsjdk.samtools.BAMFileReader.getFileSpan(BAMFileReader.java:914) at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:931) at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:612) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:550) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:417) at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.loadNextIterator(SamReaderQueryingIterator.java:130) at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.<init>(SamReaderQueryingIterator.java:69) at org.broadinstitute.hellbender.engine.ReadsPathDataSource.prepareIteratorsForTraversal(ReadsPathDataSource.java:412) at org.broadinstitute.hellbender.engine.ReadsPathDataSource.iterator(ReadsPathDataSource.java:336) at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.iterator(MultiIntervalLocalReadShard.java:134) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.<init>(AssemblyRegionIterator.java:86) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:188) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289)