Hi All,
I have encountered this strange problem while submitting a job to an sge queue. I have used the unified method wherein the galaxy setup is made available on NFS. I have mounted the galaxy directory on the execution host.
As I submit a job through the web ui I could trace that the job does get submitted to the queue. But however it fails with an error as below:
galaxy.jobs.runners.sge DEBUG 2009-04-14 08:36:09,252 (15/15) state change: job finished, but failed galaxy.jobs ERROR 2009-04-14 08:36:09,493 Unable to cleanup job 15 Traceback (most recent call last): File "/usr/galaxy/galaxy-6c555b0460f1/lib/galaxy/jobs/__init__.py", line 523, in cleanup shutil.rmtree( self.working_directory ) File "/usr/local/lib/python2.5/shutil.py", line 167, in rmtree onerror(os.listdir, path, sys.exc_info()) File "/usr/local/lib/python2.5/shutil.py", line 165, in rmtree names = os.listdir(path) OSError: [Errno 2] No such file or directory: './database/job_working_directory/15'
Where could error be. Kindly let me know if anybody has faced error before.
Thanks a ton Akash
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Akash Mohan wrote:
As I submit a job through the web ui I could trace that the job does get submitted to the queue. But however it fails with an error as below:
galaxy.jobs.runners.sge DEBUG 2009-04-14 08:36:09,252 (15/15) state change: job finished, but failed
Hi Akash,
This state is provided by the scheduler itself. Have you ensured that you can run simple jobs from the command line as the Galaxy user? If so, can you check the SGE logs to see if anything is logged when the job fails? You might also want to check the contents of the job's output/error in the database/pbs/ directory.
--nate
Hi All
Thanks Nate for your response. It helped me solve my problem. I checked the log file in SGE. It kept on throwing a warning that "unable to find shell "/bin/csh" " I, then, installed csh using yum and then, voila, the jobs were getting submitted and run.
Thanks a lot again...
Akash
-----Original Message----- From: Nate Coraor [mailto:nate@bx.psu.edu] Sent: Thursday, April 16, 2009 2:02 AM To: Akash Mohan Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Error while submitting a job to sge queue
Akash Mohan wrote:
As I submit a job through the web ui I could trace that the job does get submitted to the queue. But however it fails with an error as below:
galaxy.jobs.runners.sge DEBUG 2009-04-14 08:36:09,252 (15/15) state change: job finished, but failed
Hi Akash,
This state is provided by the scheduler itself. Have you ensured that you can run simple jobs from the command line as the Galaxy user? If so, can you check the SGE logs to see if anything is logged when the job fails? You might also want to check the contents of the job's output/error in the database/pbs/ directory.
--nate
DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.
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Akash Mohan -
Nate Coraor