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'

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)?

Thanks,


-- 
Ry4an Brase                                         612-626-6575
Software Developer                                  Application Development
University of Minnesota Supercomputing Institute    http://www.msi.umn.edu
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