These are chat archives for nextflow-io/nextflow

25th
Feb 2018
Daniel E Cook
@danielecook
Feb 25 2018 20:35
I’m having an interesting issue. We use the ‘pbs’ executor and it was working well for quite some time. Running a pipeline today though throws an error and it appears nextflow is attempting to submit the job thinking its the SLURM executor instead. I have process.executor = ‘pbs’ in my ~/.nextflow/config file and have also tested this with a local nextflow.config file...
ERROR ~ Error executing process > 'kmer_counting (BGI3-RET3b-ECA243)'

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

Command executed:

  qsub -N nf-kmer_countin .command.run

Command exit status:
  1

Command output:
  There was an error running the SLURM sbatch command.
  The command was:
  '/usr/bin/sbatch -e nf-kmer_countin.e%A -o nf-kmer_countin.o%A -J nf-kmer_countin .command.run 2>&1'
  and the output was:
  'sbatch: error: invalid partition specified: genomicsguest
   sbatch: error: Batch job submission failed: Invalid partition name specified
  '