Ry4an Brase wrote: > I'm working on getting more of our jobs offloaded to other machines, and > I'm getting job failures I'm not able to debug. When running a simple > tool like 'cut', submitted over qsub, I'm getting STDERR output like > this: > > WARNING:galaxy.datatypes.registry:Error loading datatype "binseq.zip", > problem: 'module' object has no attribute 'Binseq' > WARNING:galaxy.datatypes.registry:Error loading datatype "fastqc", > problem: 'module' object has no attribute 'fastqc' > WARNING:galaxy.datatypes.registry:Error loading datatype "ssaha2_index", > problem: 'module' object has no attribute 'SSAHA2Index'
Hi Ry4an, It looks like your datatypes_conf.xml is out of date. Have a look at the differences from datatypes_conf.xml.sample. > > and nothing on STDOUT. I'm doing the "Unified Method" as described here > https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster with > paths to datafiles and executables the same on the web runner and torque > worker systems. I can successfully qsub trivial jobs ("ls") from the > web runner machine and see them executed remotely. The web runner's > galaxy log doesn't show anything out of the norm: > > galaxy.jobs INFO 2011-02-23 16:23:55,400 JobWrapper prepare 4019 Cut1 Ry4an > perl /website/galaxy.msi.umn.edu/PRODUCTION/tools/filters/cutWrapper.pl > /galaxy/PRODUCTION/database/files/019/dataset_19366.dat "c1,c2" T > /galaxy/PRODUCTION/database/files/019/dataset_19823.dat > galaxy.jobs INFO 2011-02-23 16:24:04,559 JobWrapper state 4019 Cut1 running > Ry4an > 128.101.189.29 - - [23/Feb/2011:16:24:06 -0500] "POST > /root/history_item_updates HTTP/1.1" 200 - > "https://galaxy.msi.umn.edu/history"; "Mozilla/5.0 (X11; U; Linux x86_64; > en-US) AppleWebKit/534.13 (KHTML, like Gecko) Chrome/9.0.597.84 Safari/534.13" > galaxy.jobs INFO 2011-02-23 16:24:07,771 JobWrapper finish 4019 Cut1 error > Ry4an > galaxy.jobs INFO 2011-02-23 16:24:07,880 JobWrapper done 4019 Cut1 error > Ry4an > > I didn't see it in the Cluster config but I added the <galaxyroot>/lib > to the $PYTHONPATH just in case, but no luck. > > Is it possible it's just the output on STDERR causing the job to fail, > and if so how do I shut that up when I'm running through qsub (so > redirect to /dev/null isn't quite right)? Yes, anything output to STDERR will be considered a failure. There is a ticket in Bitbucket for this (actually, you commented on it 8 months ago ;) https://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-decide-whether-to --nate > > Thanks, > > > -- > Ry4an Brase 612-626-6575 > Software Developer Application Development > University of Minnesota Supercomputing Institute http://www.msi.umn.edu > _______________________________________________ > To manage your subscriptions to this and other Galaxy lists, please use the > interface at: > > http://lists.bx.psu.edu/ _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
