Output log file to cluster option

问题

I'm submitting jobs to slurm/sbatch via snakemake. I'm trying to send the log from sbatch to a file in the same directory tree of the rule's output.

For example, this works:

rm -rf foo
snakemake -s test.smk --jobs 1 --cluster "sbatch --output log.txt"

but it fails (i.e. slurm job status is FAILED) if I try:

rm -rf foo
snakemake -s test.smk --jobs 1 --cluster "sbatch --output {output}.log"

presumably, because {output} points to foo/bar/ which does not exist. But snakemake should have created it, right?

This is test.smk:

rule all:
    output:
        'foo/bar/done.txt'
    shell:
        """
        touch {output}
        """

So, how can I send logs to a directory tree not yet existing but created by the rule? (I'm reluctant in including code in the snakefile that create dirs in anticipation).

snakemake -v
4.8.0

来源：https://stackoverflow.com/questions/50042226/output-log-file-to-cluster-option