Hi Edgar,

I am a pretty big newbie to Galaxy but I have had similar problems on my
Dev build with grabbing outputs from the working directories. Its a
temporary fix but I have put routines in a bash wrapper that uses a working
directory that I made and know. If your cluster has access to a shared
drive that would work that way it may work.

Josh

On Thu, Sep 17, 2015 at 11:05 PM, Fernandez Edgar <
edgar.fernan...@umontreal.ca> wrote:

> Hello gents,
>
>
>
> I figured out something: it has nothing to do with galaxy but maybe one of
> you could explain me why I’m having this behavior :
>
> I connect ssh on the torque master (where the galaxy web service is
> running) and:
>
> 1.       su - galaxy
>
> 2.       cd /home/galaxy/galaxy-prod/database/job_working_directory/000
>
>
>
> I execute a job #1234, it fails with the error mentioned below.
>
> I execute the exact same job #1235 and while it’s running I enter the
> directory 1235 à job finishes successfully.
>
>
>
> My directory /home/galaxy is an nfs mount in /etc/fstab.
>
> Any ideas?
>
>
>
> Cordialement / Regards,
>
> Edgar Fernandez
>
>
>
> *De :* Fernandez Edgar
> *Envoyé :* September-17-15 9:44 AM
> *À :* galaxy-...@bx.psu.edu
> *Objet :* [galaxy-dev] need help badly
>
>
>
> Hello gents,
>
>
>
> I hope everyone is doing ok…
>
> I’m in need of your help so badly it’s a little bit urgent:
>
>
>
> So my galaxy wasn’t used in a while but the last time everything was
> working well:
>
> 1.       The web-site was functional
>
> 2.       The local handler upload the files locally on the master
>
> 3.       Torque was shooting all the jobs correctly and getting an answer
> back.
>
>
>
> But today, one of my students tried some typical trimmomatic and all his
> jobs came back with the following error:
>
> Job output not returned from cluster.
>
>
>
> However, when I checked his datasets with that error, the view data (icon
> that is an eye) had some results.
>
> Also, when I looking inside the logs, I got:
>
> Job output not returned from cluster: [Errno 2] No such file or directory:
> '/home/galaxy/galaxy-prod/database/job_working_directory/000/406/galaxy_406.o'
>
> But that file galaxy_406.o existed and had
>
> TrimmomaticPE: Completed successfully
>
>
>
> I tried changing the value from 0 to 5 of "retry_job_output_collection"
> in the config/galaxy.ini file without any success.
>
>
>
> I’ve look through the internet and I saw a lot of people had that error
> but no one found a solution.
>
>
>
> Can you guys please help?
>
>
>
> Cordialement / Regards,
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> (  Bur. : *1-514-343-6111 <1-514-343-6111> poste 16568*
>
>
>
> *Université de Montréal*
>
> PAVILLON ROGER-GAUDRY, bureau X-218
>
>
>
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-- 
Nil mihi rescribas, tu tamen ipse veni!
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