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 | [email protected] La Jolla Institute for Allergy and Immunology ----- Original Message ----- > From: "Hemant Kelkar" <[email protected]> > To: "J. Greenbaum" <[email protected]>, [email protected] > 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: [email protected] > [mailto:[email protected]] On Behalf Of J. > Greenbaum > Sent: Thursday, May 24, 2012 9:18 PM > To: [email protected] > 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 | [email protected] > La Jolla Institute for Allergy and Immunology
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