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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
