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NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
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Warning regarding path for log file #85

Closed ZoePochon closed 1 year ago

ZoePochon commented 1 year ago

It seems that this command in the rule Bowtie2_Index in align.smk log: f"logs/BOWTIE2_BUILD/{config['bowtie2_patho_db']}.log",

generates always the same warning when running the pipeline: File path logs/BOWTIE2_BUILD//proj/nobackup/metagenomics/databases/PathoGenome/library.pathogen.fna.log contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. File path logs/BOWTIE2_BUILD//proj/nobackup/metagenomics/databases/PathoGenome/library.pathogen.fna.log contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.

This is what I have in my config file: bowtie2_patho_db: /proj/nobackup/metagenomics/databases/PathoGenome/library.pathogen.fna

This would be easily fixable by getting rid of the "/" in the command itself, but I also think that the generated path is just too long for a log file no ?

FreyaStein commented 1 year ago

I seem to encounter the same Problem. Did you fix it manually in the align.smk?

ZoePochon commented 1 year ago

Hi ! Yes so far I just changed it myself in the align.smk as it was just a warning:

log: "logs/BOWTIE2_INDEX/BOWTIE2_INDEX.log",

I'm gonna ask for a merge about this.

ZoePochon commented 1 year ago

Warning fixed with the merge.