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Q:

knocking transmission on 2005 Mazda RX-8

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There is knocking coming from the manual transmission when the clutch is engaged. The sound goes away when the clutch is no longer engaged.
(1) Answer
(1) Comments
If you mean the sound happens when the clutch pedal is on the floor but goes away when you raise it and the car moves, then that sounds like it could be a possible throw out bearing that is wearing out.
If the noise happens when you are moving and your foot is off the clutch pedal, then it is an internal transmission problem.
A clutch issue is not so serious, but an internal manual transmission issue could mean it is time for a rebuilt transmission.