I couldn't find an issue for this anywhere (correct me if I am wrong).
FATES currently does not work with the CTSM/CLM nitrogen cycle, meaning that all CLM runs need to be carbon only. I undertand from @rgknox that the primary thing missing is the capability for FATES to take up N from the soil, but to do this requires some consideration of how the FATES N uptake philosphy should interact with the CTSM soil BGC model. This needs some dedicated discussion so just flagging here the need for that to happen.