If you want to do the whole processing batch, once again with no masterFlatDark but with dark optimization, you must remove the master-bias from the master-dark before:
Integrate all bias to build master-bias
Calibrate dark frames with master-bias
Integrate all calibrated darks to build master-dark
Calibrate flat frames with master-bias
Integrate all calibrated flat to build master-flat
Preprocess light frame with master-bias, master-dark and master-flat