Problems with partitions [slurm + Nextflow]

user_7580614 0
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I've tested the Nextflow's sarek pipeline in a slurm-based cluster. I'm having an error I cannot fix...

Error executing process > 'get_software_versions'
Caused by:
  Failed to submit process to grid scheduler for execution
Command executed:
  sbatch .command.run
Command exit status:
  1
Command output:
  sbatch: error: Batch job submission failed: No partition specified or system default partition

...and this is my nextflow.config file:

executor {
    name = 'slurm'
    cpus = 10
    memory = '10 GB'
    queue = 'short'
}

I guess is something related with partition assignation. I also tried change queue = 'short' by clusterOptions = '-p short', just in case, but it keeps failing.

Any idea about what I'm miss-considering, please?

partition nextflow slurm
1 Answers

Try instead setting the process.executor value to slurm in your nextflow.config:

process {

  executor = 'slurm'
  queue = 'short'
}

The executor scope just lets you set some optional executor settings. Note that if the cpus and memory settings are applied here, they will only be used with the local executor.

user_7518630
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