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Old 11-04-2010, 08:39 AM   #1
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(
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 is offline   Reply With Quote
Old 11-04-2010, 10:12 AM   #2
Location: Texas

Join Date: May 2010
Posts: 13

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.
unagaswamy is offline   Reply With Quote

bam, io error, java error, samtools

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