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-   -   Samtools IO error (http://seqanswers.com/forums/showthread.php?t=7690)

unagaswamy 11-04-2010 08:39 AM

Samtools IO error
 
Hi Experts,
I am trying to use samtools to remove duplicates and bad reads from a BAM file. I get the following IO error. Does this mean I don't have enough space for output generation?

Exception in thread "main" net.sf.samtools.util.RuntimeIOException: sync failed
at net.sf.samtools.util.BinaryCodec.close(BinaryCodec.java:594)
at net.sf.samtools.util.BlockCompressedOutputStream.close(BlockCompressedOutputStream.java:178)
at java.io.FilterOutputStream.close(FilterOutputStream.java:143)
at net.sf.samtools.util.BinaryCodec.close(BinaryCodec.java:590)
at net.sf.samtools.BAMFileWriter.finish(BAMFileWriter.java:77)
at net.sf.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:175)
at FilterBAMForSNPCalling.main(FilterBAMForSNPCalling.java:57)
Caused by: java.io.SyncFailedException: sync failed
at java.io.FileDescriptor.sync(Native Method)
at net.sf.samtools.util.BinaryCodec.close(BinaryCodec.java:588)

Thanks for your input.
Uma

unagaswamy 11-04-2010 10:12 AM

UPDATE:
This error occured because I didn't specify the directory as current in the msub command:
Quote:

echo "command"| msub -V -d `pwd`...
Moab was trying to write the output in a directory where I did not have permissions.


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