In the present invention, when trouble occurs and the operation of a substrate processing apparatus is stopped, substrate information containing positions and processing states of the substrates located in the apparatus at that time is stored, and the power supply of the apparatus is then turned off. When the apparatus is restarted, the substrates located in the apparatus are collected into a substrate housing unit, and each of the substrates in the substrate housing unit is then sequentially transferred to a plurality of processing units following the same transfer recipe as that before occurrence of trouble, and substrate processing is not performed in a processing unit in which processing has already been completed, whereas substrate processing is performed in a processing unit in which processing has not been performed yet, based on the substrate information.

 
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