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 <lucato...@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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