A processing chamber such as a plasma etch chamber can perform deposition and etch operations, where byproducts of the deposition and etch operations can build up in a vacuum pump system fluidly coupled to the processing chamber. A vacuum pump system may have multiple roughing pumps so that etch gases can be diverted a roughing pump and deposition precursors can be diverted to another roughing pump. A divert line may route unused deposition precursors through a separate roughing pump. Deposition byproducts can be prevented from forming by incorporating one or more gas ejectors or venturi pumps at an outlet of a primary pump in a vacuum pump system. Cleaning operations, such as waferless automated cleaning operations, using certain clean chemistries may remove deposition byproducts before or after etch operations.