Hi Nate, thanks a lot for your hints. I was finally able to fix the problem. Galaxy couldn?t find the .drmerr file because our SGE installation merged .drmerr into .drmout... now everything works fine! Cheers, Sascha Original Message processed by CONSOLIDATE Subject: Re: [galaxy-dev] Job output not returned from Cluster Sent: Freitag, 13. Juli 2012 19:35 From: Nate Coraor (nate@bx.psu.edu) On Jul 9, 2012, at 11:25 AM, Sascha Kastens wrote:
Hi!
Unfortunately I was not able to fix this problem yet.
Is anybody out there who had a similar problem while using Galaxy with SGE or has the knowledge about the things I can look at?
Hi Sascha, The error message you are getting is because the SGE job?s stdout and stderr files are not where Galaxy expects to find them. The working directory will be output to the debug log prior to the job?s execution and should resemble: // where: is the absolute path to the value of job_working_directory in universe_wsgi.ini is determined based on the job ID but is most likely ?000? if you are just setting up a new server is the job?s ID as shown in the debug log Upon job completion, this directory should contain files like .drmout and .drmerr. Is it possible that your SGE installation is overriding the stdout/stderr paths, or that job_working_directory is not a shared filesystem?
Thanks in advance!
Cheers, Sascha ___________________________________________________________ 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: