On Jul 9, 2012, at 11:25 AM, Sascha Kastens wrote:
> 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?
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:
<job_working_directory>/<job id hash ...>/<job id>
<job_working_directory> is the absolute path to the value of
job_working_directory in universe_wsgi.ini
<job id hash> is determined based on the job ID but is most likely '000' if
you are just setting up a new server
<job id> is the job's ID as shown in the debug log
Upon job completion, this directory should contain files like <job id>.drmout
and <job id>.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!
> 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:
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: