Using EXCEPT before WITH RECURSIVE in SQLite 3
The WITH goes first in a query. You can use this:

WITH RECURSIVE ct AS (...)
SELECT x
FROM table
EXCEPT
SELECT y
FROM ct ;


For the record, CTEs can be (in standard SQL) inside subqueries but not many DBMS have implemented this syntax:

SELECT x
FROM table
EXCEPT
SELECT y
FROM 
  ( WITH RECURSIVE ct AS (...)
    SELECT y
    FROM ct 
  ) AS c ;


or this simpler one:

SELECT x
FROM table
EXCEPT
( WITH RECURSIVE ct AS (...)
  SELECT y
  FROM ct 
) ;