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CCRGeneticsBranch / Oncogenomics_NF_WF

https://ccrgeneticsbranch.github.io/Oncogenomics_NF_WF/
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slurmstepd: error: on Biowulf #34

Closed vinegang closed 1 month ago

vinegang commented 1 month ago 
ERROR ~ Error executing process > 'Exome_only_WF:Exome_common_WF:QC_exome_bam:Coverage (RMS_JS398_2871_P)'

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: Unable to contact slurm controller (connect failure)

Work dir:
  /vf/users/khanlab/projects/processed_DATA/RMS_JS398/RMS_JS398_2871/work/7d/027d6adcbbaa87daf5303654f64837

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

slurmstepd: error: Unable to send job complete message: Unable to contact slurm controller (connect failure)

ERROR ~ Error executing process > 'Exome_only_WF:Exome_common_WF:Exome_GATK:GATK_BR_PR (RMS_JS397_2870_P)'

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: Unable to contact slurm controller (connect failure)

Work dir:
  /vf/users/khanlab/projects/processed_DATA/RMS_JS397/RMS_JS397_2870/work/33/374115bf7d83358a9b4663f1137493

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

slurmstepd: error: Unable to send job complete message: Unable to contact slurm controller (connect failure)
vinegang commented 1 month ago

slurmstepd: error: Unable to send job complete message: Unable to contact slurm controller (connect failure) these errors usually mean a glitch in the biowulf slurm system. Relaunching the job fixed the issue. Also, always report this to biowulf folks.