Hi @DorrainLow,
MaAsLin should be able to handle a large number of covariates. I have run it with at least n= 40 and been fine. Therefore, without a toy dataset with a minimally reproducible error of what you are observing, I can’t be 100% sure what the issue is. If that is not possible, can you provide the code you used to run MaAsLin? That may help me as well.
As to the second point, if you run the model with all of these fixed effects it runs them in combination. See the second part of this post for more information.
Best,
Kelsey