I noticed that one cannot calibrate Prefered flow direction using pest?

Did you get an error?

It is not even available in the options to calibrate also Runoff Resistance Factor is not there

These two variables are only available at the lowest level branches within a catchment. For example, if you have a catchment named "Farm," which has two branches, "Irrigated" and "Rainfed," then Runoff Resistance Factor and Preferred Flow Direction exist for the "Irrigated" and "Rainfed" branches, but not on the "Farm" branch. Therefore, when you are calibrating with PEST, you must choose the lowest level branch so that you can choose Runoff Resistance Factor or Preferred Flow Direction.

Jack

Thanks so much Jack I am grateful