search

franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
189 stars 41 forks source link

Fix assembly stat #96

Closed Xentrics closed 2 years ago

Xentrics commented 2 years ago

Assembly stats runs 'wc -l' on compressed fasta output. It should be decompressed prior to counting lines

franciscozorrilla commented 2 years ago

Thanks again for this fix. Although I cannot produce an error on my side when using less on the compressed fasta file, I also do not get an error when using zcat as you suggest; I will incorporate this as a failsafe.