Steve Taylor wrote:
Yes it says:
galaxy.jobs.runners.sge DEBUG 2010-04-29 15:33:33,133 (136/1221) state change: job finished normally
but in Galaxy it still is showing it as running.
After this you should also see 'job 136 ended'. This means that Galaxy has finished all post-processing.
If this never happens, please try enabling this option:
use_heartbeat = True
This will create two files:
heartbeat.log heartbeat.log.nonsleeping
Watching the latter will show what the threads are up to when this is happening. I suspect it's setting metadata, but this should tell us for sure.
--nate
Steve