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):

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
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> >  http://lists.bx.psu.edu/
>
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to