Hey Peter, Carlos, Thanks for tracking this down, I've updated the composite job/task id tag to use an underscore instead in changeset 8658:c901bbb4eca8.
-Dannon On Jan 23, 2013, at 12:00 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Thu, Jan 17, 2013 at 11:14 PM, Peter Cock <p.j.a.c...@googlemail.com> > wrote: >> >> >> 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> >>> 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 and didn't get any answer about it is related to your findings >>> while trying UGE. >>> >>> >>> 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. > > Confirmed - on our system using UGE (and likely our old system > with SGE), when task split jobs are assigned job shell scripts with > a colon in the filename it does work. However, the presence of > the colon prevents manual submission of the same script, which > I have found extremely useful in debugging. e.g. > > $ qsub sleep:colon.sh > Unable to run job: Colon (':') not allowed in objectname. > Exiting. > > Escaping the colon did not help: > > $ qsub sleep\:colon.sh > Unable to run job: Colon (':') not allowed in objectname. > Exiting. > > (Sadly the Univa Grid Engine UGE version of qsub does not > appear to have a version switch so I'm not sure which version > this is) > > For this reason alone, I would prefer Galaxy avoided colons > in its job filenames - and I suspect there could be other corner > cases with other cluster systems and shared file-systems (as > found by Carlos). > > Regards, > > Peter > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/