yes, i think galaxy already grabs these files. i seem to recall this process would get stuck if the output was too large (i was running something with a --debug/verbose option and galaxy would not finish the job even though it was off the cluster -- had to redirect to a log file).
so i guess others aren't having the same problems as i had, which is good news
On Thu, Dec 1, 2011 at 10:01 AM, Nate Coraor nate@bx.psu.edu wrote:
On Nov 29, 2011, at 9:22 PM, Fields, Christopher J wrote:
On Nov 29, 2011, at 3:13 AM, Peter Cock wrote:
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
...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.
Unless I'm misunderstanding, this is what Galaxy already does. stdout/stderr up to 32K are read from .o and .e and stored in job.stdout/job.stderr. We do need to just store them as files and make them accessible for each tool run, this will hopefully happen sometime soonish.
--nate
chris ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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