To anyone having this problem, please use the flag "--flavor bigg" when running smetana.
The problem is the way the exchange reactions are calculated. If we know the models use BiGG identifiers we can assign all reactions that start with "REX" as exchange reactions. Otherwise, it searches for all unbalanced reactions which can include internal "sink" reactions as well, and this creates an error when merging the individual species into community models.
To anyone having this problem, please use the flag "--flavor bigg" when running smetana.
The problem is the way the exchange reactions are calculated. If we know the models use BiGG identifiers we can assign all reactions that start with "REX" as exchange reactions. Otherwise, it searches for all unbalanced reactions which can include internal "sink" reactions as well, and this creates an error when merging the individual species into community models.
I will try to fix this soon.