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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(
at net.sf.samtools.util.BlockCompressedOutputStream.close(
at net.sf.samtools.util.BinaryCodec.close(
at net.sf.samtools.BAMFileWriter.finish(
at net.sf.samtools.SAMFileWriterImpl.close(
at FilterBAMForSNPCalling.main(
Caused by: sync failed
at Method)
at net.sf.samtools.util.BinaryCodec.close(

Thanks for your input.

unagaswamy 11-04-2010 10:12 AM

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

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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