SAN FRANCISCO — Thousands of commuters in the San Francisco Bay Area were scrambling for alternate routes after its regional commuter rail system known as BART shut down systemwide for several hours Friday morning.

Bay Area Rapid Transit said it could not run its train control system due to a malfunction.

A BART spokesperson said on its media phone line that they could not power up the train control system, which prevented them from being able to safely operate the trains. The cause was not immediately provided.

BART carries nearly 175,000 people on most weekdays.

The system went down shortly after 5 a.m. and service wasn’t fully restored until around 9 a.m., complicating morning commutes.

BART also runs to the San Francisco International Airport. Alternate ferry and bus service stepped up to help passengers reach their destinations.

PHOTOS: San Francisco region's commuter trains are running again after hours-long stoppage