The backup started around 6:30 a.m. when the Bay Bridge metering lights malfunctioned, causing backups approaching the toll plaza from as far back as Children's Hospital Oakland.
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"It was much, much worse than usual," said Katie Hull, who lives in Oakland and commutes into San Francisco. "I was thinking there must be an accident, must be something going on, this traffic is just backed up all over the place."
But there were no accidents, construction or lane closures.
"Just a glitch," said Caltrans spokesperson Bob Haus. "The software in the controller went out."
Haus explained the software, and the computers it runs on, are part of a system installed more than 40 years ago to control the metering lights. The lights, and their variable timing, are meant to prevent backups on the bridge -- but when the timing is wrong, it can create backups at the toll plaza. That's what happened Tuesday morning, when the lights slowed down and began staying red for too long.
"The old system actually served us well for a long time, when you figure it's 1970s vintage," Haus said. "It really didn't start giving us any problems until recently."
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Caltrans gave ABC7 News a demonstration of that system just over a year ago. Engineers monitor cameras from the Traffic Management Center in Oakland, and control the metering lights remotely using a simple desktop computer program.
"All we do is we punch in the metering rate and hit the 'Send' button, and the lights will start cycling," explained Caltrans worker Kane Wong in a November 2016 interview.
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During the malfunction, that remote control capability stopped working. Caltrans engineers had to come to the toll plaza and operate the metering lights by hand.
"For awhile, they were controlling things manually, the way they did in the old days," Haus said. "And then they were able to get things straightened out by about 9 o'clock."
Commuters say the lights don't seem to have much of a rhythm lately.
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"They just randomly turn green or red," said Shannon Woods, who commutes into San Francisco from Alameda.
"I look up, 'Is that God up there?' Just making crazy decisions, it doesn't seem like it's coordinated at all," she said.
Caltrans says there is a fix in the works. The Metropolitan Transportation Commission is leading a $7 million project to replace the metering lights with a new smart system like the ones already in place at some I-80 on-ramps.
Those systems use data from road sensors and computer vision cameras to measure traffic flow and adjust the lights automatically.
The project was initially scheduled to be finished last month, but work hasn't begun yet. Until it is, Haus said Caltrans engineers might be making more trips out to the toll plaza.
"We'll do the best we can to keep the problems down to a minimum," he said.
Before you head out to your car, be sure to check out the ABC7 traffic maps for real-time information to help you navigate through traffic jams.