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. --nate
Any ideas?
Steve