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I figured it out, it was along the lines of what mshabunin asked. I setup the application as a service, there is a "WorkingDirectory" assignment that I was missing. Once specified, it's working as it should.

[Unit] 
Description=Time lapse camera application

[Service]
WorkingDirectory=/var/www/camera/
User=root
ExecStart=/usr/bin/python3 /var/www/camera/main.py
Restart=always

[Install]
WantedBy=multi-user.target