I have installed an instance of Galaxy on our server. I configured it to run the jobs on our cluster (SGE).
Everything works just fine. I can run NGS jobs that run on our cluster nodes and return results to Galaxy.
But, sometimes, I have a problem with the job status that is not updated! It can be flagged as "waiting" and never run, or, even worst, stay flagged as "running".
When I check the logs I can see that the job has finished normally [1].
As the step is not flagged as "done" I cannot go further with my workflow.
Any help would be welcomed!
Thanks for your great work with Galaxy!
Best regards,
Tanguy LE CARROUR
[1] Galaxy logs sample:
galaxy.jobs DEBUG 2010-08-25 11:59:45,727 dispatching job 8 to sge runner
galaxy.jobs.runners.sge DEBUG 2010-08-25 11:59:47,935 (8) submitting file /srv/GT/www/htdocs/Galaxy/new_galaxy/database/pbs/galaxy_8.sh
galaxy.jobs.runners.sge DEBUG 2010-08-25 11:59:47,936 (8) command is: python /srv/GT/www/htdocs/Galaxy/new_galaxy/tools/samtools/sam_to_bam.py --input1=/srv/GT/www/htdocs/Galaxy/new_galaxy/database/files/000/dataset_9.dat --dbkey=hg19 --ref_file="None" --output1=/srv/GT/www/htdocs/Galaxy/new_galaxy/database/files/000/dataset_10.dat --index_dir=/srv/GT/www/htdocs/Galaxy/new_galaxy/tool-data
galaxy.jobs.runners.sge DEBUG 2010-08-25 11:59:47,941 (8) queued in ims.q queue as 202466
galaxy.jobs.runners.sge DEBUG 2010-08-25 11:59:48,590 (8/202466) state change: job is queued and waiting to be scheduled
galaxy.jobs.runners.sge DEBUG 2010-08-25 11:59:54,594 (8/202466) state change: job is running
galaxy.jobs.runners.sge DEBUG 2010-08-25 12:02:58,979 (8/202466) state change: process status cannot be determined
galaxy.jobs.runners.sge DEBUG 2010-08-25 12:02:59,979 (8/202466) state change: job finished normally
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Tanguy LE CARROUR
Functional Genomics Center Zurich
ETH Zurich / University of Zurich
Winterthurerstrasse 190
8057 Zurich
Switzerland