SAN FRANCISCO -- Transit officials say a "ghost train" at the Embarcadero station and a switching problem on the Peninsula have caused delays throughout Wednesday morning on Bay Area Rapid Transit.

BART spokesman Linton Johnson said that the computer system "saw" a train that did not exist at the Embarcadero BART station, forcing operators to drive trains manually.

Johnson said that trains can operate no faster than 25 mph manually, causing a backup in the Transbay Tube, used by four of the five BART lines.

The BART spokesman said that ghost trains are fairly common in the BART computer system, but it is unusual to experience delays for this long.

Trains traveling into San Francisco from the East Bay were still delayed by about 20 minutes.

Adding to the delays is an ongoing track-switching problem on the new stretch of track on the Peninsula, causing delays to San Francisco International Airport of about 20 minutes, said Johnson. He said BART has had a problem with the switching since October and the software makers have been working on permanently fixing the problem since last week.

Johnson said it was unclear how long the delays will persist.