Dear list,

I'm struggling to get jobs running on our cluster (UGE).

In the galaxy log I see: DEBUG 2017-04-13 12:24:57,799 (10) submitting file /gpfs1/data/galaxy_server/galaxy-dev/database/jobs_directory/000/10/ DEBUG 2017-04-13 12:24:57,799 (10) native specification is: -l h_rt=60 -l h_vmem=1G -pe smp 2

and I get WARNING 2017-04-13 12:24:57,805 (10) drmaa.Session.runJob() failed, will retry: code 17: error: no suitable queues

But manual submission works:

qsub -l h_rt=60 -l h_vmem=1G -pe smp 2 /gpfs1/data/galaxy_server/galaxy-dev/database/jobs_directory/000/10/
Your job 161150 ("") has been submitted

So I checked if I can use the drmaa library to submit using the following python script (based on the example2 included in the library):

#!/usr/bin/env python

from __future__ import print_function
import drmaa
import os

def main():
    """Submit a job.
    Note, need file called in current directory.
    s = drmaa.Session()
    print('Creating job template')
    jt = s.createJobTemplate()
    jt.remoteCommand = os.getcwd() + '/'
    jt.args = ['42','Simon says:']
    jt.nativeSpecification = "-l h_rt=60 -l h_vmem=1G -pe smp 2"

    jobid = s.runJob(jt)
    print('Your job has been submitted with id ' + jobid)

    print('Cleaning up')

if __name__=='__main__':

This gives me the same error:

drmaa.errors.DeniedByDrmException: code 17: error: no suitable queues

So it seems to be a problem related to the drmaa python library. Unfortunately I can not try without any native specs, since time, memory and cores need to be specifies (a suitable queue is chosen automatically).

I found an earlier post with the same error (but this seemed to be caused by colons in the file name):

Does anyone has suggestions for me?

Best regards,


Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
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Phone +49 341 235 482296,,

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