bam文件排序时出错

Runtime.totalMemory()=5838471168

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Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: Problem writing temporary file file:///work/my_reseq/tmp/sortingcollection.2676215835069172723.tmp.  Try setting TMP_DIR to a file system with lots of space.

        at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:260)

        at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:182)

        at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:202)

        at picard.sam.SortSam.doWork(SortSam.java:163)

        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289)

        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:104)

        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:114)

Caused by: htsjdk.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; streamed file (filename not available)

        at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:222)

        at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:212)

        at htsjdk.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:168)

        at htsjdk.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:40)

        at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:254)

        ... 6 more

        Suppressed: java.io.IOException: Disk quota exceeded

                at java.base/sun.nio.ch.FileDispatcherImpl.write0(Native Method)

                at java.base/sun.nio.ch.FileDispatcherImpl.write(FileDispatcherImpl.java:62)

                at java.base/sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:136)

                at java.base/sun.nio.ch.IOUtil.write(IOUtil.java:101)

                at java.base/sun.nio.ch.IOUtil.write(IOUtil.java:71)

                at java.base/sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:306)

                at java.base/sun.nio.ch.ChannelOutputStream.writeFully(ChannelOutputStream.java:68)

                at java.base/sun.nio.ch.ChannelOutputStream.write(ChannelOutputStream.java:105)

                at java.base/java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:125)

                at java.base/java.io.BufferedOutputStream.implWrite(BufferedOutputStream.java:221)

                at java.base/java.io.BufferedOutputStream.write(BufferedOutputStream.java:199)

                at org.xerial.snappy.SnappyOutputStream.dumpOutput(SnappyOutputStream.java:360)

                at org.xerial.snappy.SnappyOutputStream.compressInput(SnappyOutputStream.java:377)

                at org.xerial.snappy.SnappyOutputStream.flush(SnappyOutputStream.java:334)

                at org.xerial.snappy.SnappyOutputStream.close(SnappyOutputStream.java:419)

                at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:259)

                ... 6 more

Caused by: java.io.IOException: Disk quota exceeded

        at java.base/sun.nio.ch.FileDispatcherImpl.write0(Native Method)

        at java.base/sun.nio.ch.FileDispatcherImpl.write(FileDispatcherImpl.java:62)

        at java.base/sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:136)

        at java.base/sun.nio.ch.IOUtil.write(IOUtil.java:101)

        at java.base/sun.nio.ch.IOUtil.write(IOUtil.java:71)

        at java.base/sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:306)

        at java.base/sun.nio.ch.ChannelOutputStream.writeFully(ChannelOutputStream.java:68)

        at java.base/sun.nio.ch.ChannelOutputStream.write(ChannelOutputStream.java:105)

        at java.base/java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:125)

        at java.base/java.io.BufferedOutputStream.implWrite(BufferedOutputStream.java:221)

        at java.base/java.io.BufferedOutputStream.write(BufferedOutputStream.java:199)

        at org.xerial.snappy.SnappyOutputStream.dumpOutput(SnappyOutputStream.java:360)

        at org.xerial.snappy.SnappyOutputStream.compressInput(SnappyOutputStream.java:377)

        at org.xerial.snappy.SnappyOutputStream.write(SnappyOutputStream.java:130)

        at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:220)

        ... 10 more

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1 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

硬盘存储不够了,需要扩大存储,或者删除一些数据再分析;

Disk quota exceeded

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