It appears when variables are set in aux_outputs in a yaml config file for SA_setup_and_run.py the dimensions are not correctly set. An example of this is VEGC y p c, but I have also had trouble on the add_methane branch too. It looks like this command only outputs VEGC by pft and not compartment. The issue on the add_methane branch is due to outputting variables by month and by layer, but only getting by month.