Warehouse with a storage and retrieval system

A storage and retrieval system (400) including a vertical array of storage levels, each storage level having, picking aisles (130F), storage locations, disposed within the picking aisles (130F), and at least one transfer deck (330A,330B) providing access to the picking aisles (130F), a multilevel vertical conveyor system configured to transport the uncontained case units to and from the vertical array of storage levels, each storage level being configured to receive uncontained case units from the multilevel vertical conveyor system, at least one autonomous transport (110) located on each storage level for transporting the uncontained case units between respective storage locations and the multilevel vertical conveyor system, and a controller configured to create a primary access path through the transfer decks (330A,330B) and picking aisles to a predetermined one of the storage locations and at least one secondary access path to the predetermined one of the storage locations when the primary path is impassable.