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Old 08-09-2010, 09:48 AM   #1
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Location: Boston area

Join Date: Nov 2007
Posts: 747
Default bwa sampe hanging

I'll apologize for asking what amounts to a pre-question; I know I really don't have a complete description to the problem but I'm a little stumped how to get some more useful descriptive information.

I am running bwa (0.5.8a) on 4 GAIIx lanes of paired-end human sequence. The machine is a 64bit x86 machine with 32Gb of RAM and running Oracle Enterprise Linux (aka Red Hat Enterprise Linux 5, a sore subject, but the state of things).

Generation of the .sai files using "bwa align" works fine, but for three out of the four lanes, the program is hanging during the "bwa sampe" stage. As far as I can tell, it will stay running for hours with no further output.

If I split the FASTQ files at about the last sequence which is output, then the program completes for each fraction and I can merge the alignment SAM files with samtools -- but it's definitely an extra step I'd prefer to avoid. But that does suggest that it isn't a simple aberrant FASTQ entry which is the trigger.

Any suggestions for further info I should spelunk that would be useful for troubleshooting this? Is there a good way to determine whether the .sai files are somehow corrupt? Anyone seen something (an odd character?) in a FASTQ file which can sometimes be troublesome?

thanks in advance
krobison is offline   Reply With Quote