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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> 


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