Hi Nate, I tried to help Luca today, but I failed totally ... He is not using <param id="nativeSpecification"> at all. Or put it that way if he isn't using it, he gets the same error. Cheers, Bjoern Am 02.04.2014 20:34, schrieb Nate Coraor:
Hi Luca,
Are you passing any params to the runner for inclusion as PBS submit parameters (<param id="nativeSpecification"> in job_conf.xml)?
--nate
On Wed, Apr 2, 2014 at 12:59 PM, Luca Toldo <lucatoldo@gmail.com> wrote:
Dear all, SUSE SLE 11 SP 1, with PBS Pro 12.1 client delivers
galaxy.jobs.runners ERROR 2014-04-02 18:28:43,740 (249) Unhandled exception calling queue_job Traceback (most recent call last): File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 62, in run_next method(arg) File "/opt/ngs/bin/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 151, in queue_job external_job_id = self.ds.runJob(jt) File "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/__init__.py", line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/helpers.py", line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer)))) File "/opt/ngs/bin/galaxy-dist/eggs/drmaa-0.6-py2.6.egg/drmaa/errors.py", line 90, in error_check raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value)) InvalidAttributeValueException: code 14: Illegal attribute or resource value: Illegal attribute or resource value
If I do qsub -q NGSq /opt/ngs/bin/galaxy-dist/database/job_working_directory/000/249/galaxy_249.sh
however the qsub returns
12345.myserver
and the corresponding
qstat | grep -i galaxy 12345.myserver galaxy_249.sh galaxy 00:00:00 E NGSq
Is the above error message perhaps related with a) PBS 12.1 b) drmaa-0.7-py2.6.egg
I am trying to compile pbs-drmaa-1.0.17 but there are problems ...
any advice ?
any alternative ?
Thanks luca
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