htsjdk.samtools.util.RuntimeIOException

java.io.IOException: No space left on device

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Solutions on the web6

  • java.io.IOException: No space left on device
  • via broadinstitute.org by Unknown author, 1 year ago
    java.io.IOException: No space left on device
  • via broadinstitute.org by Unknown author, 4 months ago
    java.io.IOException: No space left on device
  • Stack trace

    • htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:245) at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:165) at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:281) at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:114) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206) 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:318) 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:236) ... 6 more

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