Substrate processing apparatus, substrate processing method and storage medium

Disclosed is a substrate processing apparatus in which a target substrate is taken out from a slot of a cassette having a plurality of slots and processed. The substrate processing apparatus includes a substrate processing unit that processes the target substrate, a transfer unit that transfers the target substrate from the cassette to the substrate processing unit and transfers the target substrate processed in the substrate processing unit from the substrate processing unit to the cassette, and a confirming unit that determines whether or not the slot is empty. The substrate processing apparatus further includes a control unit that reads the slot designated to the target substrate and makes the confirming unit to determine whether or not the slot is empty, after the target substrate has been processed in the substrate processing unit but before the target substrate is disposed in the cassette.