On Nov 8, 2011, at 6:34 PM, Andrew Warren wrote:
> Hi Nate,
>
> I am running in daemon mode so this out of paster.log.
>
> The job gets submitted to the PBS queue normally but the error shows up in
> history panel right away (also the working directory shows up during the
> cufflinks run):
Hi Andrew,
The job should not even be able to be submitted to the PBS queue. The error
you're seeing in the history (Unable to run job due to a misconfiguration of
the Galaxy job running system. Please contact a site administrator.) is logged
when the job manager tries to place the job in the queue of a job runner which
has been defined in the Galaxy configuration but has not properly loaded. This
is right after a statement which should log the failure:
log.error( 'put(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id,
runner_name ) )
I'm not sure how that message could not appear in the log when the associated
message is appearing in the history item. Can you confirm that the output
below was for a job that immediately failed with the above error message? By
any chance, are you running multiple Galaxy servers simultaneously with job
running enabled?
--nate
> galaxy.jobs DEBUG 2011-10-24 17:51:25,567 dispatching job 595 to pbs runner
> galaxy.jobs INFO 2011-10-24 17:51:25,772 job 595 dispatched
> galaxy.jobs.runners.pbs DEBUG 2011-10-24 17:51:26,153 (595) submitting file
> /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/pbs/595.sh
> galaxy.jobs.runners.pbs DEBUG 2011-10-24 17:51:26,155 (595) command is:
> python
> /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/tools/ngs_rna/cufflinks_wrapper.py
>
> --input=/opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/files/001/dataset_1866.dat
>
> --assembled-isoforms-output=/opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/files/002/dataset_2161.dat
> --num-threads="6" -I 300000 -F 0.05
> -j 0.05 -g
> /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/files/001/dataset_1699.dat
> -b
> --ref_file=/opt/rnaseq_data/indices/bowtie/Salmonella/14028S/Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_14028S.fna
> --dbkey=14028S
> --index_dir=/opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/tool-data
> galaxy.jobs.runners.pbs DEBUG 2011-10-24 17:51:26,157 (595) queued in batch
> queue as 303.localhost
> galaxy.jobs DEBUG 2011-10-24 17:51:26,599 dispatching job 596 to pbs runner
> galaxy.jobs INFO 2011-10-24 17:51:26,738 job 596
> dispatchedgalaxy.jobs.runners.pbs DEBUG 2011-10-24 17:51:26,767
> (595/303.localhost) PBS job state changed from N to R
>
> Then later with no errors in paster.log when the cufflinks job is finishing
> (notice that it doesn't try to copy the contents of the working directory for
> this job like it normally does because galaxy thinks the job wasn't submitted
> to the queue even though it was):
>
> galaxy.jobs.runners.pbs DEBUG 2011-10-24 19:05:57,402 (595/303.localhost) PBS
> job has left queue
> galaxy.jobs.runners.pbs DEBUG 2011-10-24 19:05:57,402 (596/304.localhost) PBS
> job state changed from Q to R
> galaxy.jobs.runners.pbs DEBUG 2011-10-24 21:29:01,995 (596/304.localhost) PBS
> job has left queue
> galaxy.jobs.runners.pbs DEBUG 2011-10-24 21:29:01,995 (597/305.localhost) PBS
> job state changed from Q to R
> galaxy.jobs DEBUG 2011-10-24 21:29:02,999 finish(): Moved
> /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/job_working_directory/596/isoforms.fpkm_tracking
> to
> /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/files/002/dataset_2163.dat
> as directed by from_work_dir
> galaxy.jobs DEBUG 2011-10-24 21:29:03,555 finish(): Moved
> /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/job_working_directory/596/genes.fpkm_tracking
> to
> /opt/hts_software/galaxy-parent/galaxy_server/galaxy-dist/database/files/002/dataset_2162.dat
> as directed by from_work_dir
>
> Thanks,
> Andrew
>
> On Mon, Nov 7, 2011 at 4:00 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> On Oct 25, 2011, at 2:43 AM, Andrew Warren wrote:
>
> > Hello,
> > I recently encountered a problem when trying to run Cufflinks on eight BAM
> > files on our galaxy instance (via the multi-input toggle) and received the
> > error: "Unable to run job due to a misconfiguration of the Galaxy job
> > running system" for some, but not all, of the cufflinks jobs that appear in
> > the history. These particular BAM files were copied over from the history
> > of a larger workflow where they were successfully run through cufflinks. In
> > the case of the problem workflow run, the cufflinks jobs are all
> > successfully submitted to Torque PBS and continue to run and finish but
> > many have this error displayed in the History. The jobs with the error
> > displayed fail to copy files from the working directory to the database
> > directory despite running to completion. We recently updated to
> > galaxy-central changeset 6131:be6c89c33639. I have seen this error multiple
> > times for this workflow, even after restarting galaxy. Does anyone have any
> > ideas of what might be going wrong?
>
> Hi Andrew,
>
> The error you're receiving indicates that there should also be a traceback
> logged to the Galaxy server log file or output when this occurs. Could you
> check the log/output for such a traceback?
>
> Thanks,
> --nate
>
> >
> > Thanks for any help,
> > Andrew Warren
> > ___________________________________________________________
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