"use_heartbeat = True" is set. No heartbeat log files are generated after restarting Galaxy service and running a queue job. Zong-Pei On Thu, 29 Apr 2010, Nate Coraor wrote: Date: Thu, 29 Apr 2010 16:03:59 +0100 From: Nate Coraor <nate@bx.psu.edu> To: Stephen Taylor <stephen.taylor@imm.ox.ac.uk> Cc: "galaxy-dev@bx.psu.edu" <galaxy-dev@bx.psu.edu>, "zph@herald.ox.ac.uk" <zph@herald.ox.ac.uk> Subject: Re: [galaxy-dev] Job Control in Galaxy 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