Try to execute it with a query which returns fewer rows to see if you have any other problems. After you make it work, try your query.
Also there is a difference between Run Statement and Run Script.
In the following query
spool '/home/atilla/file.txt'
SELECT * FROM DUAL;
SPOOL OFF
If I use Run Statement, I get following file
> SELECT * FROM DUAL
If I use Run Script, I get following file
> SELECT * FROM DUAL
DUMMY
-----
X
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