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]:Why, when I use CarveMe for gap-filling, does it show that my custom medium does not exist in the database? #145

Closed microbial-cookie closed 9 months ago

microbial-cookie commented 9 months ago

Hi developer,

I have been trying to construct microbial genome-level metabolic models using GEM recently. However, I encountered an issue during gap-filling, indicating that my custom medium, which I defined based on the BIGG metabolite database and existing culture medium components, does not exist in the original database. As a result, I am uncertain whether the .xml file I generated during the construction process has been gap-filled according to my custom medium. Below are images of the code and workflow I used. Although I obtained the .xml file, I am unsure if the result is correct and why it is indicating that my medium does not exist in database. Happy new year!!!

Ruiwen

image image

franciscozorrilla commented 9 months ago

Hi @microbial-cookie, the errors are related to the fact that you are using the wrong flags/parameters. More specifically, you are missing the media database flag --mediadb, and you are incorrectly using the --gapfill flag which should be specifying a media compostion in your database. Please have a look at the help message or look at this tutorial for further reference.