Navigate to the MySQL directory on cPanel

cd /var/lib/mysql/

Run ls -l to find your file

ls -l

Clear the contents of the MySQL Error Log and Log File

cat /dev/null > /var/lib/mysql/mysql.server.com.err

cat /dev/null > /var/lib/mysql/mysql.server.com.log

Check the files are empty

ls -l mysql.server.com.err

ls -l mysql.server.com.log