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problem with jobname renaming in slurm config #816

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LeoWelter opened this issue Dec 5, 2024 · 1 comment
Closed

problem with jobname renaming in slurm config #816

LeoWelter opened this issue Dec 5, 2024 · 1 comment

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@LeoWelter
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I have the following definition in my profile. Yet the parenthesis in the job names are not replaced.

executor {
            name = 'slurm'
            queueSize = 70
            submitRateLimit = '10 sec'
            jobName = {
                n = "${task.name}" -> n.replaceAll('[():\\\s]', '_')
            }
        }

therefore I get these kind of errors:


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


Command executed:

  sbatch .command.run

Command exit status:
  1

Command output:
  sbatch: error: Illegal character in job name at position 27. Valid characters are lowercase a to z, uppercase A to Z, numbers 0 to 9, period (.), underscore (_), forward slash (/) and hyphen (-).
  sbatch: error: Batch job submission failed: Unspecified error

If I look at the .command.run file, the job name is set to:
#SBATCH -J nf-NFCORE_MAG_MAG_MEGAHIT_(sample1)

I tried the java regex on https://regex101.com/ where it replaces the parenthesis correctly.

Any help to get this working is appreciated

@LeoWelter
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LeoWelter commented Dec 5, 2024

Never mind, The renaming scheme was inside the profile section, overwritten by a different config. Please close

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