You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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)
The text was updated successfully, but these errors were encountered:
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)
The text was updated successfully, but these errors were encountered: