SAN JOSE (KCBS) — A power outage caused by a squirrel threw a wrench in Caltrain’s dispatching network Wednesday morning, causing major system-wide delays on the transit system, according to the agency.

Caltrain was one of several Bay Area rail transit systems plagued by system delays Wednesday morning.

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Aside from the outage in San Jose near the Caltrain Rail Operation Center, Caltrain’s backup generator also took time to kick in. Some trains had to stop completely at stations, while others were able to continue on their way.

Caltrain spokeswoman Jayme Ackemann said the problem was not with the generator, but with a battery. “The powered battery, that keeps the system operational while we make the transition to the backup generator, failed,” she said.

Ackman said Caltrain was still trying to figure out exactly why the battery failed.

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The computer dispatch system was back up and running around 9:30 a.m., though Caltrain expected significant delays throughout the morning commute, said Caltrain spokesperson Christine Dunn.

Wednesday was a difficult transportation day in the Bay Area.  Bay Area Rapid Transit has been having equipment problems throughout the morning, causing delays.

Shortly after 7:30 a.m., a Capitol Corridor Amtrak train hit and injured a pedestrian in Crockett, near the intersection of Winslow and Vallejo streets.  The extent of the person’s injuries are unclear, but train service was delayed.

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There were also reported delays for passengers taking Altamont Corridor Express trains, possibly due to another power outage.