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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