problem with PHP_SELF

I think I found the problem.

I see this variable being set:
PHP_SELF=/opt/project/app/index.php
                               ^
But this is not where my index.php is. It is in /opt/app/index.php. It seems that all the paths to my config files has that extra /project in them. 

Where is that path with the term "project" coming from?

CodeIgniter-3.1.11/system/core/Input.php:
  651: // Sanitize PHP_SELF
  652: $_SERVER['PHP_SELF'] = strip_tags($_SERVER['PHP_SELF']);


Edit:
Have you hard-coded the following variables?

CodeIgniter-3.1.11/application/config/config.php -> $config['base_url'] = '';
CodeIgniter-3.1.11/application/config/config.php -> $config['index_page'] = 'index.php';