[galaxy-dev] BWA sampe runs 'forever'

2011-07-29 Thread Assaf Gordon
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

Re: [galaxy-dev] BWA sampe runs 'forever'

2011-07-29 Thread Assaf Gordon
Chris Fields wrote, On 07/29/2011 12:35 PM: On Jul 29, 2011, at 11:00 AM, Assaf Gordon wrote: Question for galaxy maintainers: have you encountered situations where BWA jobs run 'forever' (for days) ? ... I'm wondering if this is common enough to justify adding -A to the wrapper, or is it

Re: [galaxy-dev] BWA sampe runs 'forever'

2011-07-29 Thread Chris Fields
On Jul 29, 2011, at 12:44 PM, Assaf Gordon wrote: Chris Fields wrote, On 07/29/2011 12:35 PM: On Jul 29, 2011, at 11:00 AM, Assaf Gordon wrote: Question for galaxy maintainers: have you encountered situations where BWA jobs run 'forever' (for days) ? ... I'm wondering if this is common