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
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