SCRIPT_FILENAME is missing error with cron

On cPanel server, I have my cron set as:

 php -q /home/user/public_html/filerun/cron/make_thumbs.php

For debugging I have set email notification turned on and receiving emails with error:

SCRIPT_FILENAME is missing

Same with paths_cleanup.php

However, if I run the command from the terminal, they are executing fine.