Oops you've accidently started your controller with root user i nstead of your app service user (ie appd, appdynamics, etc...) ?
1. First stop controller (as root)
2. As root, change permissions back to original user and group
chown -R <original user>:<original group> <controller home>
Ie: chown -R appd:appd /opt/appdynamics/controller
3. Start controller with your original user.
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