search

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
389 stars 88 forks source link

snakePipes 3.0.0 logging #1051

Open katsikora opened 2 months ago

katsikora commented 2 months ago

I get no logs, and the numbered run logs are empty.

WardDeb commented 2 months ago

Hi Katarzyna,

Can you add a reproducible example ? I can then have a look.

katsikora commented 2 months ago

Hi Ward,

I finally got the logs but only after the run has exit... Is this expected?

Best,

Katarzyna

WardDeb commented 2 months ago

Yea, I got rid of it when simplifying runAndCleanup. I figured real time stdout/stderr in console is enough information, and we don't need to flush the buffer on every line. In case you want this back one could just add f.flush() again after writing a line: https://github.com/maxplanck-ie/snakepipes/blob/0d30e2f7a9bb49ccf556f6f95c4c431091002316/snakePipes/common_functions.py#L738

katsikora commented 2 months ago

Hmmm, interesting, so the buffer must be quite large. Perhaps indeed flushing after each line would be useful. I'd prefer to have the log available as soon as possible if I'm working on fixing something.

thomasmanke commented 2 weeks ago

is the same information not visible under .snakemake/log/ ?