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Use caution when running scripts for jobs that have also been linked for direct database access.  The SFT client will run the script before it handles the direct database access.  If the script writes to the file to be transferred, the direct database access will overwrite the output of the script because it will write to the same file.

Generally you will use one (scripting) or the other (direct DB access), or neither, but seldom both.  The SFT client will allow you to configure it to use both, as there may be valid reasons for running a script ahead of accessing the database.