On Jul 29, 2011, at 11:00 AM, Assaf Gordon wrote:
Hello,
Question for galaxy maintainers: have you encountered situations where BWA jobs run 'forever' (for days) ?
A little digging shows that it's the "bwa sampe" step, and SEQanswers thread mention it's somewhat common: http://seqanswers.com/forums/showthread.php?t=11652 http://seqanswers.com/forums/showthread.php?t=6340
One suggested work-around is to add "-A" to "bwa sampe", but there's no way to do it in the current BWA wrapper. (On the command-line with the same input files it does make things much faster).
I'm wondering if this is common enough to justify adding "-A" to the wrapper, or is it rare enough and can be ignored.
-gordon
Can it be added as an optional argument? So that if it is selected, the setting is passed to the tool, otherwise not. chris