Invalid SyntaxWarning: invalid escape sequence

[erfanshekarriz]

Snakemake Version: 8.25.5

When running snakemake I get the following SyntaxWarning: invalid escape sequence warning:

~/workflow/rules/viral-identify.smk:273: SyntaxWarning: invalid escape sequence '\s'
  combined=relpath("identify/viral/output/combined.final.vOTUs.fa"),
~/workflow/rules/viral-identify.smk:299: SyntaxWarning: invalid escape sequence '\s'
~/workflow/rules/viral-identify.smk:606: SyntaxWarning: invalid escape sequence '\d'
~/workflow/rules/viral-identify.smk:635: SyntaxWarning: invalid escape sequence '\d'

In my .smk file's shell directive I'm using "\s" and "\d" regex characters, so I know this is where the warning comes from:

Rule 1

shell:
"""
...
seqkit grep {input.fna} -f {output.hits} | seqkit replace -p  "\s.*" -r "" | seqkit replace -p $ -r _{wildcards.sample_id}  > {params.tmpdir}/tmp.fa 2> {log}
...
"""

Rule 2

shell:
"""
...
seqkit replace {input.provirusfasta} --f-use-regexp -p "(.+)_\d\s.+$" -r '$1' | seqkit grep -f {input.provirushits} > {params.tmpdir}/tmp1.fa 2> {log}
seqkit replace {input.virusfasta} --f-use-regexp -p "(.+)_\d\s.+$" -r '$1' |  seqkit grep -f {input.provirushits} >> {params.tmpdir}/tmp1.fa 2> {log}
...
"""

But, when I run with the -p flag, it prints my commands fine and it also runs fine, so I don't want to change my code:

Rule 1

shell:
"""
...
seqkit grep sample/contigs/results/identify/viral/intermediate/scores/combined.viralcontigs.fa -f sample/contigs/results/identify/viral/output/derep/cluster_representatives.txt > sample/contigs/results/identify/viral/tmp/tmp.fa 2> sample/contigs/results/identify/viral/logs/clustering/filterderep.log
...
"""

Rule 2

shell:
"""
...
seqkit grep sample/contigs/results/identify/viral/output/checkv/viruses.fna -f sample/contigs/results/identify/viral/output/virus.list.txt > sample/contigs/results/identify/viral/tmp/tmp2.fa 2> sample/contigs/results/identify/viral/logs/vOTUs.log
seqkit grep sample/contigs/results/identify/viral/output/checkv/proviruses.fna -f sample/contigs/results/identify/viral/output/virus.list.txt >> sample/contigs/results/identify/viral/tmp/tmp2.fa 2> sample/contigs/results/identify/viral/logs/vOTUs.log
...
"""

I've double-checked and the shell command works as it should. It likely has to do with the way Snakemake parsers the shell command.

I was not experiencing this with the older version of Snakemake 7.28.1, just popped up as I updated it!

Is there a good way to bypass or suppress the warning?

Best,
Erfan

[rwanwork]

@erfanshekarriz Just a comment... I just encounter this bug as well on version 7.32.4 (the current version for Ubuntu 24.10). I noticed the warning goes away when double backslashes are used. i.e., \\d+.

I'm not sure if it is a bug or maybe we need to just escape backslashes from now on.