On Thursday, January 17, 2013, Carlos Borroto wrote: > On Wed, Jan 16, 2013 at 7:28 AM, Peter Cock > <p.j.a.c...@googlemail.com<javascript:;>> > wrote: > >> Renaming the file to replace the colon with (say) an underscore allows > >> a manual qsub to work fine with UGE. I've edited Galaxy to avoid the > >> colons (patch below) but the submission still fails. > >> > > Hi Peter, > > After seeing your email I now wonder if the problem I described > here[1] and didn't get any answer about it is related to your findings > while trying UGE. > > [1] > http://dev.list.galaxyproject.org/Issue-when-enabling-use-tasked-jobs-with-torque-and-nfs-td4657294.html > > I noticed the only mayor different I can notice between jobs > submission with and without tasked option enabled is a colon in the > name. >
Some overlap yes, and I do normally have BLAST running with task splitting. That does probably explain the source of the colon. I now suspect the colon is only a problem in SGE / UGE at the command line using qsub - it may work via the Python API. I have also seen some similar problems with sub-jobs failing yet Galaxy still had the task as a green success (not sure if that has happens recently or not). Yesterday while our UGE cluster was under load, often one or more of my split task jobs would fail (Galaxy could not collect the output files - presumably network related for accessing the shared storage), but Galaxy was correctly flagging these as red failed jobs. Cluster problems are hard to debug - especially on a live cluster where there are other users active :( Peter
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