Ammonia is nitrogen on the move. Urea, chicken manure, cotton seed cake and every other nitrogen source breaks down during Phase I, and the nitrogen leaves the material as ammonia. This is normal. DMR reports compost at the end of Phase I holding about 800 to 1,000 ppm, with pH pushed up to roughly 8.2 to 8.5.
The size of your ammonia problem is therefore decided long before the tunnel. DMR notes that a mix carrying more than 1.75 percent nitrogen loses more of it as ammonia, and that such compost attracts yellow moulds, ink caps and olive green mould.