It happened after midnight on Fresno-Coalinga Road and El Dorado Avenue, south of Five Points.
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California Highway Patrol officers say the driver of the truck carrying tomatoes ran the stop sign at Oakland Avenue, which is connected to both roads.
The tomato truck collided with a semi carrying grapes that had turned.
The crash caused a massive spill at the intersection.
The grape truck was T-boned, and the driver of the tomato truck was pinned inside his cab.
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He was freed from the truck and flown by helicopter to a Fresno hospital with major injuries.
The other driver was not hurt.
Officers say the scene should be cleaned up soon, and traffic has not been affected.