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snakemake / snakemake-executor-plugin-cluster-generic

Generic cluster executor for Snakemake
MIT License
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How to use `--cluster-generic-cancel-cmd` on LSF #17

Open keviny2 opened 6 months ago

keviny2 commented 6 months ago

My Snakefile looks like this,

rule test:
    output:
        "test.txt"
    resources:
        mem_mb=4000
    shell:
        "sleep 600 && touch {output}"

and my config.yaml file looks like,

executor: cluster-generic
cluster-generic-submit-cmd: 'bsub -R "rusage[mem={resources.mem_mb}GB]" -n 4'
cluster-generic-cancel-cmd: bkill

I fire up my workflow with snakemake --profile profile/ and then press ^C to terminate the process early. I get the following warning,

Job <36740856> is submitted to default queue <long>.: Illegal job ID.
1 out of 1 calls to --cluster-cancel failed. This is safe to ignore in most cases.

and the job isn't terminated. What am I missing?

I am using snakemake v8.11.3.