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OLC-Bioinformatics / ConFindr

Intra-species bacterial contamination detection
https://olc-bioinformatics.github.io/ConFindr/
MIT License
22 stars 8 forks source link

Error when running confindr.py #18

Closed anacristinareis closed 1 year ago

anacristinareis commented 4 years ago

Hello,

When I try to run ConFindr the following error occurs: File "/Users/miniconda3/lib/python3.7/site-packages/confindr_src/confindr.py", line 1045, in confindr min_matching_hashes=min_matching_hashes) File "/Users/miniconda3/lib/python3.7/site-packages/confindr_src/confindr.py", line 767, in find_contamination out, err = run_cmd(cmd) File "/Users/miniconda3/lib/python3.7/site-packages/confindr_src/confindr.py", line 33, in run_cmd raise subprocess.CalledProcessError(p.returncode, cmd=cmd)

The command I'm running: confindr.py -i ./ -o ./results -d ./Databases_Confindr

I do not know how to solve this problem.

Thanks

adamkoziol commented 3 years ago

Hi! Your command should work as written, so that isn't the problem. What sequences are you trying to process? I've updated ConFindr to version 0.7.3 on bioconda. Are you willing to try the new version and see if you are getting the same error message?

Thanks!

anacristinareis commented 3 years ago

Hi,

Sorry, for the late response. Your suggestion sove the problem.

Thanks for all your help.