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did you run the “register a retroarch controller” option?

you can also test controllers by installing jstest:
sudo apt-get install joystick

then use it like this:
jstest /dev/input/js0
jstest /dev/input/js1
jstest /dev/input/js2
jstest /dev/input/js3

the numbers at the end are for each controller that is connected

hope you enjoy playing your games