Hi Hermant,

Thanks for the suggestion. I've tried setting that parameter to 5, but it has 
not helped. I've noticed in the galaxy server output that I'm getting the 
following error:

galaxy.jobs.runners.pbs DEBUG 2012-05-25 08:13:17,957 (96) pbs_submit failed, 
PBS error 15031: Protocol (ASN.1) error

I believe this is why certain jobs are failing. I've googled a bit for this 
error, and found many threads where similar problems were reported. Here are a 
couple:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-February/004336.html
http://osdir.com/ml/galaxy-development-source-control/2011-02/msg00148.html

Is anyone aware of a solution to this issue?

Thanks,

J

-- Jason Greenbaum, Ph.D.
Manager, Bioinformatics Core | jgb...@liai.org
La Jolla Institute for Allergy and Immunology

----- Original Message -----

> From: "Hemant Kelkar" <hkel...@unc.edu>
> To: "J. Greenbaum" <jgb...@liai.org>, galaxy-dev@lists.bx.psu.edu
> Sent: Friday, May 25, 2012 4:34:12 AM
> Subject: RE: [galaxy-dev] possible to resume failed workflow?

> Jason,

> Are the affected workflow steps actually failing or are they falsely
> being reported as “failed” (have you checked if correct output
> exists for the affected step)? Once a step/job is marked “failed’
> you can’t use the output (even if it exists) for any subsequent
> step.

> If you are using a cluster for your local galaxy install and NFS disk
> mounts then this may happen because of write cache delays. If that
> is the case, increasing the value for the
> “retry_job_output_collection” parameter to a higher number in the
> universe_wsgi.ini should help you get around the problem. It fixed
> the problem in our local galaxy where some jobs were being reported
> as “failed” though the correct output was there.

> --Hemant

> From: galaxy-dev-boun...@lists.bx.psu.edu
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of J.
> Greenbaum
> Sent: Thursday, May 24, 2012 9:18 PM
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] possible to resume failed workflow?

> Hi,

> I've created a few workflows and have been having issues with some
> steps randomly failing. This would not be an issue if I could simply
> resume the workflow from the failed step, but it seems that this is
> not possible. Instead, I'm forced to restart the workflow from the
> beginning. Is this true or am I missing something?

> Thanks,

> Jason

> --
> Jason Greenbaum, Ph.D.
> Manager, Bioinformatics Core | jgb...@liai.org
> La Jolla Institute for Allergy and Immunology
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