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.
On Thu, Sep 17, 2015 at 11:05 PM, Fernandez Edgar <
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
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.
Cordialement / Regards,
*De :* Fernandez Edgar
*Envoyé :* September-17-15 9:44 AM
*À :* galaxy-dev(a)bx.psu.edu
*Objet :* [galaxy-dev] need help badly
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
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
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:
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,
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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