This question is a bit outdated but I thought I’d post how I resolved this issue when it happened to me on my Mac (OS X El Capitan 10.11.4).
Check the status just to be sure
ERROR! MySQL is running but PID file could not be found
Find all running mysql processes
ps aux | grep mysql
It will list out all the processes using mysql (including the command you just executed)
Kill off all the mysql pids
sudo kill <pid1> <pid2> <pid3> ...
This should kill off all the mysql processes
Now try to fire mysql up
Hope this helps someone!
EDIT: Alternative solution from @DanielTate
This worked for me JasperSoft Wiki – uninstall-mysql-mac-os-x. I had to brew uninstall mysql then delete ALL of the files then reinstall and follow the home brew install instructions
EDIT 2: Alternative solution from @JanacMeena
There is a nice write-up of their solution in this post on Medium.