Security locked up?

There are couple different ways to do this, first roll the windows up and use the ignition key to lock the driver's door and allow it to sit overnight and then unlock the door using the key, if that doesn't work I would do the hard system reboot which is done by removing the negative side of the battery, with the cable loose from the negative side of the battery, hold it to the positive terminal for 1 minute this will discharge the memory capacitors in the BCM and PCM allowing the system to reboot.

Please check out this guide as well:

https://www.2carpros.com/articles/how-to-reset-a-security-system

Let me know how it goes. You can't clear the security system using a scanner, you can only read the codes.