it should have been done automatically on first reboot after the unlock portion of the tool. unless you did not reboot and went straight into flashing twrp.I don't remember doing a factory reset with the stock recovery but I did a factory reset with the TWRP recovery.
2 options that may help.
option 1
1 boot to fastboot mode
2 type "fastboot format userdata"
3 type "fastboot format cache"
4 reboot --either "fastboot reboot" if not work then long hold power button
option 2
1 boot to fastboot mode
2 type "fastboot boot stock-recovery.img"
3 if there is "trapped" command that needs to be run it should do so without input from you