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Old 11-04-2010, 08:39 AM   #1
unagaswamy
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Location: Texas

Join Date: May 2010
Posts: 13
Default 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
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Old 11-04-2010, 10:12 AM   #2
unagaswamy
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Location: Texas

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Default

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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