It happened Thursday at the Merced Church of Christ on Highway 140 and Edwards Avenue.
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Church leaders say a canister light in the ceiling of the main auditorium shorted out and smoldered overnight.
The light fell over and triggered the security system at about 6 a.m.
That's when a pastor went to check on what was happening.
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He found smoke coming from the building and called for firefighters, which helped prevent more damage.
The church will not hold services until it passes a city inspection.