My jobs have this problem when the command for the tool is wrapped by the 
stderr wrapper script.

Ka Ming
________________________________________
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
On Behalf Of Edward Kirton [eskir...@lbl.gov]
Sent: July 28, 2011 3:41 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] "Job output not returned from cluster"

I've been getting these errors sometimes lately, particularly when the cluster 
is heavily loaded.  The jobs have completed successfully, as I can see the 
output if I click the pen icon, but the job is in a failed state.

Have any other sites been experiencing this problem?
Or can the galaxy developers help shed some light on the issue?

FYI, I use the outputs_to_working_directory option in universe_wsgi.ini so that 
i can use a faster/more reliable filesystem to collect output from the cluster. 
 I'm not using the recently discussed patch to run jobs as the unix user.

I'll continue to experiment with different filesystems and software settings.


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