chpst permission issues when trying to run gitlab-ctl reconfigure and gitlab-rails console

Whenever I try to run the above two commands, I get "chpst: fatal: unable to run: /opt/gitlab/embedded/bin/bundle: permission denied".

I've tried changing ownership/access of said file and reinstalling chpst because /usr/bin/chpst originally didn't exist. Server is running Ubuntu 18.04.

Because of these errors I am unable to get reply by email working and from installation of the GitLab server I have to reboot the server anytime I want to change gitlab.rb as unicorn fails to restart due to this error.