...in our case amino acids, which are actually part of the biomass reaction.
The report provides the missing biomass building blocks as metanetX ids. It seems like there is some mapping issue from these metanetX ids to other ids.
In short, memote seems unable to identify specific amino acids from their corresponding KEGG IDs. Could be an issue with the heuristics here or our shortlist being outdated, or it could be that there are duplicates/ isoforms of the offending metabolites with overlapping annotations.
It could also be an issue with the IDs used in the original model. It would be easiest to debug if @anushcph could share the model.
Opening on behalf of @anushcph
Problem description
In short, memote seems unable to identify specific amino acids from their corresponding KEGG IDs. Could be an issue with the heuristics here or our shortlist being outdated, or it could be that there are duplicates/ isoforms of the offending metabolites with overlapping annotations.
It could also be an issue with the IDs used in the original model. It would be easiest to debug if @anushcph could share the model.