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The Seven Trees Community Center has been housing victims of the Coyote Creek flood since February.
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At least 60 people are still there and will be forced out Monday.
The city will be able to put some people in hotels and motels for 30 days at a time.
VIDEO: Aerial tour of flood damage in San Jose
The housing department is working on affordable housing options for those residents who are unable to return to their homes.
Flood victims in need should call Catholic Charities at (408) 468-0100.