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Tag Archive for pythonslurmsnakemakehpc

Snakemake fails with executor SLURM with slurm_persist_conn_open_without_init

PROBLEM When I use snakemake with a cluster profile and leave it running overnight, trying both with a screen process or with a nohup snakemake … & detachment, I will run into the following error below for each currently running rule/job: The job status query failed with command: sacct -X –parsable2 –noheader –format=JobIdRaw,State –starttime 2024-06-06T03:00 […]