Sounds an awful lot like march haemoglobinuria to me - nothing to do with the time of the year of course! It's basically lots and lots and lots of running can sometimes mash RBCs to bits in your feet as they constantly pass through, freeing haemoglobin and giving rise to the haematuria you've experienced. It is a transient problem, which obviously desists when you stop running. Might be best to double check it with your GP but I am fairly certain this is what's happened to you unless you've experienced any other unusual symptoms
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