The following MySQL command will show you long-running processes (exceeding 5 seconds in this case).
select * from information_schema.processlist where command <> 'sleep' and time > 5;
You can run it from console to view those happening now, or you could make a script to poll it periodically, with something like:
echo "select * from information_schema.processlist where command <> 'sleep' and time > 5;" | mysql > long-running.log
(See also https://serverfault.com/questions/416380/log-slow-queries-killed-before-completion/858093)