Why was Kokura not bombed with the second atomic bomb?

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Kokura was not bombed with the second atomic bomb because thick clouds and haze obscured the city, preventing the bombardier from sighting the designated aimpoint.12

On August 9, 1945, the crew of the B-29 Bockscar made three unsuccessful attempts to bomb the city's massive arsenal. After lingering over the area for roughly 45 minutes, concerns regarding diminishing fuel reserves and the threat of Japanese antiaircraft defenses led the mission's weaponeer, Comdr. Frederick Ashworth, to conclude that they must proceed to the secondary target, Nagasaki.1