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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

[Bug]: 'BiGG_gene' is both an index level and a column label, which is ambiguous. #137

Closed Baizhou12138 closed 1 year ago

Baizhou12138 commented 1 year ago

Hi Professor. I'm a newbie and I'm trying to construct a community metabolic model using carveme in order to analyze the metabolic characteristics of the community using smetana solver.I already had the data fasta file from the commercial company that handles the annotated data, so I decided to start with step 6 of the workflow. I am encountering some strange erro's that report errors as follows: unnamed im not sure where the peoblems are and how to fix that.Oh,In addition, I will show you my fasta file format if it will help you to understand. unnamed unnamed I have about 9,000 similar files that need to be analyzed at the same time.what should i do?QAQ I would really appreciate it if you could give me a guide.Thanks again.

Baizhou12138 commented 1 year ago

I'm wondering if I can use my existing annotated fasta file to directly perform the "Reconstruct & evaluate genome-scale metabolic models with CarveMe and memote" and "Species metabolic coupling analysis with SMETANA" in the workflow. Please let me know if my question is not clear enough. i'm really looking forward to your help. thanks again.

franciscozorrilla commented 1 year ago

Hey Baizhou, thanks for posting your issue with screenshots and explanations. I believe that this is not a bug, rather you are providing CarveMe with the incorrect input file. You need to translate the DNA to protein and perform open reading frame (ORF) annotation. For reference have a look at the following tutorial https://github.com/franciscozorrilla/EMBOMicroCom/blob/main/exercises/exercise_4.md

winnieLu-cup commented 4 months ago

Hey Baizhou, thanks for posting your issue with screenshots and explanations. I believe that this is not a bug, rather you are providing CarveMe with the incorrect input file. You need to translate the DNA to protein and perform open reading frame (ORF) annotation. For reference have a look at the following tutorial https://github.com/franciscozorrilla/EMBOMicroCom/blob/main/exercises/exercise_4.md

follow the turorial, and mistakes still exist. Is it possible that CarveMe is incompatible with the versions of python, diamond, and solver? image image

franciscozorrilla commented 4 months ago

Hi @winnieLu-cup, it looks like your input file is now correct, I am not sure why the error is occuring. It does not seem to be a common issues topic on the CarveMe github repo, it could be buggy behavior related to the recently added SCIP solver, maybe you could try with cplex academic version instead?