On Monday, November 28, 2011, Joseph Hargitai <joseph.hargitai@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