Running drush as regular user I've recently upgraded to Drush 8, from Drush 6.2 (That was installed using pear).

Drush on cPanel runs fine as root, but when I try to run it as a regular user in a valid Drupal directory I get the error: 

Command pm-refresh needs a higher bootstrap level to run - you will need to invoke drush from a more functional Drupal environment to run[error]


this command

Or for just trying to clear cache using drush cc all:

No Drupal site found, only 'drush' cache was cleared


And when I add --debug to the end of a command I get a mysql error with drush:

Access denied for user 'username'@'localhost'
I was able to get to the bottom of this problem.  When I ran drush in debug mode, for example "drush status --debug" it outputted an error that it could not connect to the database.  

After hours of digging for some reason on this particular cPanel server there were .my.cnf files in each user's home directory which contained mysql authentication details.  Drush was taking precedence on these credentials and in turn not able to connect to the particular Drupal install's database.  I simply did "rm -rf /home/username/.my.cnf to delete each of these hidden files, then running drush works!