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alesssia / YAMP

YAMP: Yet Another Metagenomic Pipeline
GNU General Public License v3.0
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SGE cluster queue specification #15

Open CRichard21 opened 4 years ago

CRichard21 commented 4 years ago

Hello,

I am trying to run YAMP on a cluster of type SGE. It put these information in "process" part of the nextflow.config file :

executor = 'sge' queue = 'batch,batchbm'

I get the following error : 

`Error executing process > 'qualityAssessment (1)'

Caused by:
  Failed to submit process to grid scheduler for execution

Command executed:

  qsub -terse .command.run

Command exit status:
  1

Command output:
  Unable to run job: "job" denied: use parallel environments instead of requesting slots expl
  Exiting.`

I think the problem comes from the fact that in a normal use, I need to specify the queue on this cluster as follow : qsub -q queue myscript

How can I solve this problem ?

Thanks,

Corentin

alesssia commented 4 years ago

Hi @CRichard21,

my guess is that you need to specify the parallel environment (e.g., mpi) within the nextflow.config file, using the penv directive.

You could also compare one of your SGE scripts with that generated by nextflow (.command.run in the working directory that failed), and see if you can spot any other issues.

ramakrishnas commented 3 years ago

Hi @CRichard21,

I'm having the same error, so if you found a solution could you share here please.

Thanks Rama