search

alexmsalmeida / virsearch

Snakemake workflow to detect and classify viruses in metagenome assemblies.
MIT License
18 stars 4 forks source link

/usr/bin/env: ‘python2’: No such file or directory #1

Closed slambrechts closed 2 years ago

slambrechts commented 2 years ago

Hi,

Thanks for sharing this pipeline! I seem to get some /usr/bin/env: ‘python2’: No such file or directory errors while running snakemake --use-conda -k -j 48. I'm guessing this has something to do with the configuration of python, snakemake or conda on our HPC? This does not happen with my other snakemake pipelines. Can I ask what snakemake version you use for this pipeline?

Best, Sam

alexmsalmeida commented 2 years ago

Hi Sam, no problem!

I am almost certain this is due to the rename_multifasta_prefix.py script. I changed it to be compatible with python3 by default. Either reclone the repo or just replace that script with the new version. Let me know if you encounter further issues.

For future reference, I am using v6.3.0 of Snakemake.

Best, Alex

slambrechts commented 2 years ago

Hi Alex,

Yes, I think you are right! After recloning the repo, this error did not appear again. Thank you!

Best, Sam