On Monday, November 28, 2011, Joseph Hargitai <
joseph.hargi...@einstein.yu.edu> wrote:
> Ed,
>
> we had the classic goof on our cluster with this. 4 nodes could not see
the /home/galaxy folder due to a missing entry in /etc/fstab. When the jobs
hit those nodes (which explains the randomness) we got the error message.
>
> Bothersome was the lack of good logs to go on. The error message was too
generic - however I discovered that Galaxy was depositing the error and our
messages in the /pbs folder and you could briefly read them before they got
deleted. There the message was the classic SGE input/output message -
/home/galaxy.... file not found.
>
> Hence my follow up question - how can I have galaxy NOT to delete these
SGE error and out files?
>
> best,
> joe

Better yet, Galaxy should read the SGE o and e files and record their
contents as it would for a directly executed tools stdout and stderr.

Peter
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