[galaxy-dev] BWA sampe runs 'forever'

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