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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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I meet some errors when I use CarveMe for gap-filling #193

Open microbial-cookie opened 6 months ago

microbial-cookie commented 6 months ago

Hi Daniel,

After I run the gap-filling command using my defined medium, I meet errors, as below:

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please help me, thank you very much, Happy new year!!!

Ql-cy commented 5 months ago

Hi, have you solved it? I have met the same issue with a defined medium, four columns and all compound ids are from BiGG database. I have test the LB medium provided with "carve protein.faa --gapfill LB --mediadb test.tsv -o test.xml" and it works, but it would get a error while I delet one compound in the LB mediafile. So I am not sure there are regulations generating the medium file.

cdanielmachado commented 5 months ago

It is possible that you have removed something that was essential for growth. Make sure not to remove any of the inorganic compounds.

Ql-cy commented 4 months ago

Hi Daniel， I also have a question about the LB medium. Does the LB medium provided in Carveme consist of yeast extract, tryptone, H2O，oxygen, and NaCl? If I remove H+，H2O，Na+ and Cl-, can the remaining components be considered as the nutritional components of yeast extract and tryptone? I noticed there are purines, AMP and CMP, which are not typically reported in yeast extract according to the literature.

cdanielmachado commented 4 months ago

Yes, ideally the LB composition tries to represent yeast extract. It might not me completely accurate. These compounds represent intracellular yeast metabolites that, in principle, should be present in the extract.