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I recently set up a 40g tank with a fluval C4 filter. I ran the C4 on my established 55 for two weeks before filling up the 40 and switching the filter over and adding 3 small fish to test (N. Brevis) After 3 days there was a small amount of ammonia (0.25ppm) I did about a 40% water change and it has been 0 ammonia 0 nitrite ever since, so I would say run it for 2-3 weeks and you should be good.
 
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