How to fix phone always booting into recovery even when system exists

I installed CM 14.1 on a Nexus 6 and the first update booted into TWRP automatically to install but failed. I manually installed the zip from the cmupdater folder and rebooted. Now every time I try to reboot my phone or power it on from powered off it goes straight into TWRP. Currently I have to boot into the bootloader and choose the Start option to get into my system. Tried clearing dalvik/cache & internal storage in case something was cached somewhere. No dice.