Create table as takes hours

I'm doing a query that uses similarity functions to fuzzy match columns in a table against itself. Its pretty expensive as its essentially cartesian joins though I do have some equality matches to help out. It takes about 3 minutes to run.

However I executed a create table as (query) command and that 3 minute query took 14 hours to run, which it did eventually finish. I want to change the parameters of my similarity but I feel there has to be a way to reduce the difference in time between the query execution and the create table execution.

Any ideas?