localrules with --cluster and --immediate-submit are not executed locally

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Issue #1126 new
Martin Porsch created an issue

I call snakemake with snakemake -k -p --use-conda --cluster "sbatch --job-name={cluster.job-name} --cpus-per-task={threads} --output={cluster.output} --error={cluster.error} --partition={cluster.partition} --time={cluster.time} --mem={cluster.mem} \$(parseJobID.sh {dependencies})" -j 10000 --cluster-config cluster.yaml --cluster-status slurm_status.py --immediate-submit --notemp

But the localrule all is in the end submitted to the cluster-engine:

[Mon Feb 25 12:40:18 2019]
localrule all:
    input: results/qa/multiqc/fastqc_raw.html, results/qa/multiqc/fastqc_adapter_trimmed.html, results/qa/multiqc/fastqc_quality_t
rimmed.html, results/qa/multiqc/star--gtf_adj_Crubella_183_quality_trimmed.html, results/qa/multiqc/star--gtf_adj_Crubella_183_qua
lity_trimmed.html, results/de/edgeR--gtf_adj/Crubella_183/quality_trimmed/tpms.csv, results/de/edgeR--gtf_adj/Crubella_183/quality
_trimmed/tpms.genes.csv
    jobid: 0

Submitted job 0 with external jobid 'Submitted batch job 6335759'.
Complete log: /home/adswd/projects/floral_transition_capsella_rubella/.snakemake/log/2019-02-25T123926.819405.snakemake.log

Comments (2)

  1. Elise Larsonneur

    Hi @johanneskoester

    The --cluster --immediate-submit options don't work with the checkpoint example, in snakemake versions: 5.4.1 5.4.3 :

    • The rule/checkpoint chain clustering => aggregate => all is executed instead of clustering => intermediate => aggregate => all.

    • And same problem than @Kubiac : The local rule all is not executed locally and instead is submitted as a cluster job.

    The --cluster --immediate-submit options worked with dynamic and wildcards in snakemake 4.8.0.

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