The binary logs can use lots of storage space. Following are 2 ways to clean them up, by name and by time.
To remove all binary logs up to mysql-bin.003456:
mysql> PURGE BINARY LOGS TO 'mysql-bin.003456';
To remove all binary logs by date/time (Before December 8th, 2016 @6:00):
mysql> PURGE BINARY LOGS BEFORE '2016-12-08 00:06:00';
Search for MySQL binary logs, error logs, temporary files:
# lsof -nc mysqld | grep -vE '(.so(..*)?$|.frm|.MY?|.ibd|ib_logfile|ibdata|TCP)'