1. A method for controlling a semiconductor manufacturing apparatus for processing wafers divided for each lot, comprising: acquiring quality control value data group containing quality control value data of wafers in a plurality of lots previously processed by the semiconductor manufacturing apparatus, and equipment engineering system parameter group containing equipment engineering system parameters corresponding to the wafers in the plurality of lots; creating a prediction formula of quality control value data which is a Partial Least Squares (PLS) regression formula, by PLS regression on the basis of the quality control value data group and the equipment engineering system parameter group; acquiring first equipment engineering system parameters corresponding to wafers in a first lot newly processed subsequently to the last processed lot; inputting the first equipment engineering system parameters to the prediction formula, and performing calculation to predict first quality control value data of the wafers in the first lot; on the basis of the predicted first quality control value data, determining processing of the wafers corresponding to the first quality control value data, the processing to be performed by the semiconductor manufacturing apparatus; acquiring measured first quality control value data of the wafers in the first lot; replacing the quality control value data corresponding to the wafers in the first processed lot in the quality control value data group, with the first quality control value data, and replacing the equipment engineering system parameters corresponding to the wafers in the first processed lot in the equipment engineering system parameter group with the first equipment engineering system parameter; updating the prediction formula by the PLS regression on the basis of the quality control value data group and the equipment engineering system parameter group, the groups being obtained by the replacement; and when there is a second lot to be processed subsequently to the first lot, acquiring second equipment engineering system parameters corresponding to wafers in the second lot, and inputting the second equipment engineering system parameters to the updated prediction formula, and performing calculation to predict second quality control value data of the wafers in the second lot.