不知道你运行的命令,可能是输入文件格式哪里有问题吧
老师您好,我在合并gvcf时,程序刚运行一会就会自行终止,以下是出现的代码。请问如何解决?谢谢!
at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:257)
at htsjdk.tribble.readers.PositionalBufferedStream.fill(PositionalBufferedStream.java:132)
at htsjdk.tribble.readers.PositionalBufferedStream.read(PositionalBufferedStream.java:84)
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
at java.io.InputStreamReader.read(InputStreamReader.java:184)
at htsjdk.tribble.readers.LongLineBufferedReader.fill(LongLineBufferedReader.java:140)
at htsjdk.tribble.readers.LongLineBufferedReader.readLine(LongLineBufferedReader.java:300)
at htsjdk.tribble.readers.LongLineBufferedReader.readLine(LongLineBufferedReader.java:356)
at htsjdk.tribble.readers.SynchronousLineReader.readLine(SynchronousLineReader.java:51)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:170)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:205)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:149)
at org.broadinstitute.hellbender.engine.MultiVariantDataSource$1.next(MultiVariantDataSource.java:408)
at org.broadinstitute.hellbender.engine.MultiVariantDataSource$1.next(MultiVariantDataSource.java:393)
at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71)
at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57)
at htsjdk.samtools.util.MergingIterator.next(MergingIterator.java:101)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:136)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:165)
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)