I meet some errors when I use CarveMe for gap-filling

[microbial-cookie]

Hi Daniel,

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

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

[Ql-cy]

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]

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]

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]

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.