Output column mismatch. User defined SQL query in Source Qualifier

The Logic 

1) The number of fields selected in the SQL override query should match the number the number of ports in the Source qualifier which are LINKED to the next transformation. The names are not required to be the same but order needs to be the same.

Interestingly Informatica maps the fields from the SQL query to the Source qualifier output links instead of Source Qualifier ports. So the first column in the SQL query gets mapped to the first link, the second column to the second link and so on.

2) Also, all the ports in the Source Qualifier transformation need to be linked with the Source definition.