On 29/04/2010 15:54, Steve Taylor wrote:
On 29/04/2010 15:43, Nate Coraor wrote:
Steve Taylor wrote:
Trying another samtool...in the Galaxy History the job is still running (yellow background), but is finished according to SGE and there appears to be some output produced.
galaxy.jobs.runners.sge DEBUG 2010-04-29 15:32:26,051 (136) submitting file /wwwdata/galaxy-dist/database/pbs/galaxy_136.sh galaxy.jobs.runners.sge DEBUG 2010-04-29 15:32:26,052 (136) command is: python /wwwdata/galaxy-dist/tools/samtools/sam2interval.py --input_sam_file=/wwwdata/galaxy-dist/database/files/000/dataset_153.dat -p> /wwwdata/galaxy-dist/database/files/000/dataset_210.dat
That's only the initial step - you should see quite a few more with the SGE job id and state changes, and a "job finished" message once complete.
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.
Ok. It has finally completed. Maybe I am being too impatient :-). I'll run a SAM-BAM test overnight to see if it really is just a big lag! Steve