On Fri, Jul 29, 2011 at 1:01 AM, Ka Ming Nip <km...@bcgsc.ca> wrote:
> My jobs have this problem when the command for the tool is wrapped by the 
> stderr wrapper script.
>
> Ka Ming

Which stderr wrapper script? I think there is more than one...

I've also had this error message (I'm currently working out how to
connect our Galaxy to our cluster), and in at least one case it was
caused by a file permission problem - the tool appeared to run but
could not write the output files.

If Galaxy could give more diagnostics rather than just "Job output
not returned from cluster" it would help. For instance, as we use SGE,
perhaps the captured stdout/stderr files might be available.

Peter
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