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someone help me

phermyphermy South AfricaMember

[Mon Nov 14 14:47:57 SAST 2016] picard.sam.SortSam done. Elapsed time: 75.95 minutes.
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:246)
at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:166)
at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:192)
at picard.sam.SortSam.doWork(SortSam.java:92)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:326)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
at org.xerial.snappy.SnappyOutputStream.dump(SnappyOutputStream.java:127)
at org.xerial.snappy.SnappyOutputStream.flush(SnappyOutputStream.java:100)
at org.xerial.snappy.SnappyOutputStream.close(SnappyOutputStream.java:137)
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:237)
... 6 more

Issue · Github
by Sheila

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  • trevorconleytrevorconley San DiegoMember

    I'm not sure what the question is that you're asking, unless you are just looking to determine why you're receiving this error; it is stated in the error message that there is no space left on the device. This means that the hard drive you're using to do your processing has no more room to write.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @phermy Check that you have enough drive space, as @trevorconley recommends. Also, you may need to set a temp directory explicitly, as that can often be a limitation as well. If you're not sure how to do this, you can ask your IT support team; they should be able to help you.

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