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warnings with nanoasv --dry-run #107

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frederic-mahe opened this issue Nov 14, 2024 · 2 comments · May be fixed by #112
Open

warnings with nanoasv --dry-run #107

frederic-mahe opened this issue Nov 14, 2024 · 2 comments · May be fixed by #112

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@frederic-mahe
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frederic-mahe commented Nov 14, 2024 •
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(running on a fresh ubuntu-server-24-04, with Miniconda3)

/home/fred/NanoASV/workflow/run.sh: line 252: [: missing `]'
Checking reference format
/home/fred/NanoASV/workflow/snakefile:200: SyntaxWarning: invalid escape sequence '\+'
  "tmp_files/08_phylogeny/.phylogeny.done"
/home/fred/NanoASV/workflow/snakefile:222: SyntaxWarning: invalid escape sequence '\+'
  "tmp_files/.export.done"

same thing with nanoasv --mock
@ImagoXV
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ImagoXV commented Nov 15, 2024 •
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I know, I'm not sure what is triggering this warning.
Maybe the fact that those are hidden files ?
I can remove the hidden status, it does not matter, it is in tmp files in the end

Edit :
Removing hidden status didn't cure

/home/user/NanoASV/workflow/snakefile:223: SyntaxWarning: invalid escape sequence '\+' 
"tmp_files/export.done"

And there is "+" sign in those lines neither.

The only + written in code is

in snakemake file :
grep -o '[^ ]\+$' tmp_files/06_sam_to_bam_format/{wildcards.barcode}_abundance.tsv > {output.ASV_list}
But it is currently on lines 115 and 118. They have no link with the error and should be safe.

If you have any idea, I'm taking

@ImagoXV
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ImagoXV commented Nov 15, 2024

For line 252 related error, it comes from the way I wrote echo functions. This is fixed in d70701a and a37c736

@frederic-mahe frederic-mahe linked a pull request Nov 16, 2024 that will close this issue
fix SyntaxWarning: invalid escape sequence '\+' (issue #107) #112
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fix SyntaxWarning: invalid escape sequence '\+' (issue #107) ImagoXV/NanoASV
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@frederic-mahe @ImagoXV