Snakemake workflow "inconsistent use of tabs and spaces in indentation" error ?

[jnesme]

Hi Jakob ! Trying to run the handy snakemake from reads to bins in MAGinator but I am soon hitting this problem which seems to be an odd Pythin syntax error :

snakemake --use-conda -s MAGinator/maginator/recommended_workflow/reads_to_bins.Snakefile --resources mem_gb=180 --config reads=reads.csv --cores 10 --printshellcmds

returns :

TabError in file <string>, line 308:
inconsistent use of tabs and spaces in indentation (<string>, line 308)
  File "/home/projects/ku_00041/apps/jnesme/miniconda3/envs/maginator/lib/python3.12/tokenize.py", line 541, in _generate_tokens_from_c_tokenizer
  File "/home/projects/ku_00041/apps/jnesme/miniconda3/envs/maginator/lib/python3.12/tokenize.py", line 537, in _generate_tokens_from_c_tokenizer

Do you have any idea if this is a simple fix or I should just run the recommended workflow stepwise ? Best, Joseph.

[Russel88]

Hi Joseph! In what part of the workflow do you get this error?

[jnesme]

Hi Jakob, thanks a lot for taking the time to look at this ! Actually the error pops up in 4-5s after launching the above-mentioned command and the "input" I give is only the reads.csv I am working on Computerome 2.0, MAGinator is installed in its own conda env with pip and I load VAMB from computerome tools library.

[Russel88]

I just pushed a commit to the dev branch that should fix it (although I haven't tested it)

[jnesme]

Fixed, as far as I could test (and after manually installing Biopython which is not installed by pip install maginator) - at least it's building DAG of jobs, I killed it because I was on the head node 🙈 , will submit to queue and report here.

Thanks a lot Jakob

[Russel88]

Great! Yeah, we should probably remove the biopython dependency. The goal is that maginator should only have snakemake and mamba as dependencies and the rest is installed by snakemake on the fly