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

[Question]: How to use the GEM output of CarveMe to generate these two files? #149

Closed microbial-cookie closed 8 months ago

microbial-cookie commented 8 months ago

Hi franciscozorrilla,

I used the command like this (for i in *.faa do carve $i --fbc2 --gapfill LB --mediadb media-LB.tsv -o $i-LB-model.xml done) to generate the GEM files. But I didn't find these two files. Could you tell me about the command to generate these files? I think it is important for my following results. Thanks a lot!

image

franciscozorrilla commented 8 months ago

Please read the CarveMe documentation to understand the expected output, CarveMe will not produce those files for you, but you can generate them based on the GEM output + cobrapy/reframed + some scripting. If you have questions about the cheese study data/code, please raise an issue in that repository and I will be happy to help.