On Nov 29, 2011, at 3:13 AM, Peter Cock wrote:

> 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

...or at least have the option to do so, maybe a level of verbosity.  I have 
been bitten by lack of stderr output myself, where having it might have saved 
some manual debugging.

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