DBI connect('mysql:localhost','root',...) failed: Access denied for user 'root'@'localhost' (using password: YES) at /usr/local/cpanel/Cpanel/Mysql.pm line

root user was missing from mysql user table and cPanel error log was reporting following error on creating new database:

DBI connect('mysql:localhost','root',...) failed: Access denied for user 'root'@'localhost' (using password: YES) at /usr/local/cpanel/Cpanel/Mysql.pm line 37

Added root user to mysql, reset the password, specified the root password in /root/.my.cnf and got it fixed