Emergency crews responded to the scene around 3 p.m. about a half mile east of Port Costa.
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Amtrak officials say there are no immediate reports of injuries among the 55 passengers and crew that were on the train when it hit the tree.
They say the train did remain upright and that all systems were operating after the incident.
Officials say there is an adjacent track that is open and service will single track through this area.
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Stay with ABC7 News for the latest details on this developing story.