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The timeout is how long the SFT client will wait when issuing your query to the database before giving up.  The default is 10 minutes.  You may override this default by putting a value greater than 10 minutes in the Timeout field.  If you leave the field blank, or enter anything less than 10 minutes, the timeout used will be the default of 10 minutes.  (Therefore, you have only the option of increasing the timeout should you encounter exceptionally long-running queries).  The timeout is specified per query, so you may override the timeout for one query, but not another, for instance.