Cost of Auxiliary Commodity

[Antti-L]

I would like to know whether the model assign a cost also to auxiliary commodity flows, or the overall cost of a process (capital+operational) is carried only by the primary commodity output.

Can you clarify the question a bit?  
You can define variable costs on the process activity, or on specific process flows, or both. Capital costs, fixed O&M costs and decommissioning costs are defined on the process capacity.  Start-up costs can be defined on started-up capacity, and ramping costs can be defined on activity ramping (difference of activity level between successive timeslices). The overall cost of a process thus includes all these components, and the various cost components are "carried by" the variables involved (VAR_ACT, VAR_FLO, VAR_NCAP, and VAR_IRE, when applicable).

You can specify variable costs also on auxiliary commodity flows of processes, by using FLO_COST / FLO_DELIV. Which kind of auxiliary flows are you referring to?