It tries to connect to the MySQL server but it doesn't find the server where it thinks it is.
There's a good chance your MySQL server is off after the update, or the port is wrong - try this:

service mysql status

what does it print? if it's off, you may have to restart the server using sudo service mysql start.

Can you log in using the user credentials in your orthomcl.config?

mysql -u YOUR_USER -p

(enter password)

Type this:

mysql> SHOW VARIABLES LIKE 'port';

Does it print:

+---------------+-------+    
| Variable_name | Value |
+---------------+-------+
| port          | 3306  |
+---------------+-------+
1 row in set (0.16 sec)

By default, mysql runs on port 3306, but your above command indicates that your orthomcl.config looks for port 3307. Try changing the value to 3306.