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
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'
and nothing on STDOUT. I'm doing the "Unified Method" as described here
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
/galaxy/PRODUCTION/database/files/019/dataset_19366.dat "c1,c2" T
galaxy.jobs INFO 2011-02-23 16:24:04,559 JobWrapper state 4019 Cut1 running
126.96.36.199 - - [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
galaxy.jobs INFO 2011-02-23 16:24:07,880 JobWrapper done 4019 Cut1 error
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)?
Ry4an Brase 612-626-6575
Software Developer Application Development
University of Minnesota Supercomputing Institute http://www.msi.umn.edu
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