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
Runtime.totalMemory()=5838471168
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
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