In the present work, a semi-transverse ventilation system in a long tunnel with a length of 4.9 km, as a complex case study, is numerically studied by performing a set of three-dimensional steady incompressible computational fluid dynamics (CFD) simulations. The ventilation system consisted of a ceiling duct connected to two axial fans at the ending portals, and a series of jet fans in the main tunnel for supporting airflow in the desired direction. To focus on what can and cannot be achieved in commissioning tests, the ventilation system's performance in various scenarios is numerically evaluated with two different tunnel states; empty tunnel and complete traffic congestion with 1176 stationary vehicles - which is almost impossible to evaluate during a commissioning test. By considering two hypothetical locations for the extraction zone from the main tunnel (in a distance of 450 and 1000 m from one portal), it is shown that the required number of jet fans in a traffic condition drops from 57 for the first extraction location to 43 (25% decrease) when the ventilation system extracts from the second zone. We show that if only the close axial fan to the extraction zone is activated, the required number of jet fans reduces by 56% and 72% for the first and second extraction locations, respectively. This finding can provide a cheaper and easier controlling scenario for emergency ventilation.