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  • An ACE commuter train car that derailed lies in the...

    An ACE commuter train car that derailed lies in the Alameda Creek along Niles Canyon Road, in Sunol, Calif., Tuesday, March 8, 2016. Authorities said that nine of the more than 200 passengers on the Stockton-bound train were injured, four seriously. (Anda Chu/Bay Area News Group)

  • Investigators take a look over the wreckage of the derailed...

    Investigators take a look over the wreckage of the derailed ACE train No. 10 along Niles Canyon Rd. near Sunol, Calif., on Tuesday, March 8, 2016. The train ran off of the tracks Monday evening after striking a tree that had fallen during Monday's storm. (Gary Reyes/Bay Area News Group)

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SUNOL — The morning after an Altamont Corridor Express train derailed, tumbling into a rain-swollen creek with more than 200 passengers aboard, authorities said a mudslide may have triggered the crash.

The San Jose-to-Stockton line will resume Wednesday morning after crews used cranes and flatbed trucks to pull and upright the submerged car from Alameda Creek Tuesday on Niles Canyon Road between Fremont and Pleasanton.

ACE train No. 10 went off the tracks around 7:30 p.m. Monday after running into mud and debris, including a tree, authorities said. On its website, ACE said a mudslide caused the derailment and that the wheels of a second car were submerged in mud.

Nine people were injured and officials said it was “an absolute miracle” no one was killed. Four of the injuries were serious, though not thought to be life-threatening, and those passengers were taken to Eden Medical Center in Castro Valley and Washington Hospital in Fremont, according to the Alameda County Fire Department.

As of Tuesday evening, only a 24-year-old man remained hospitalized at Washington in good condition.

Officials with Union Pacific Railroad, which is investigating the crash, said Tuesday that it was clear a mudslide had toppled a tree and sent the train off the tracks, but officials were still investigating the initial point of impact.

The Federal Railroad Administration is the lead investigator on the derailment, a spokesman for said Tuesday. “We have staff on site and they are leading the investigation,” the spokesman, Mathew Lehner said. Preliminary information may be released later in the day, he said. The California Public Utilities Commission, which regulates all railroads in the state, is also investigating.

The National Transportation Safety Board, which often investigates such derailments, said Tuesday morning they will not probe the derailment.

“Based on the early information it appears it was weather-related,” said spokesman Keith Holloway. “There doesn’t appear to be much mystery as to what happened.”

The agency does not respond to every derailment, but focuses on ones with fatalities, potential safety issues and unknown causes, he said.

Union Pacific spokesman Francisco Castillo said that while it indeed appears that a mudslide caused the derailment, it wasn’t known whether the mud flowed onto the tracks before ACE train No. 10 got to that spot in the canyon, or whether it struck the lead rail car broadside as the train rolled past.

“That’s part of the investigation,” Castillo said.

First responders said it was not raining at the time of the derailment, but the Fremont area received 2.13 inches of rain since March 1, according to the National Weather Service. Roger Gass, a NWS meteorologist said a flash flood and urban and small stream advisory expired early Monday after a large series of El Nino-fueled storms smacked the Bay Area.

“It was the preceding conditions over the weekend that would have caused the ground to become saturated in that area,” Gass said.

Using two large cranes, crews started pulling the submerged lead car out of Alameda Creek about 2:45 p.m. The other four cars had been moved down along the track. The train began moving around 5:20 p.m. to the Union Pacific yard in Fremont for inspection, according to ACE spokesman Brian Schmidt.

ACE trains operate in “push-pull” mode; its trains headed from San Jose to Stockton are in “push” mode, with the locomotive pushing the cars. The engineer was in the car that ended up in the creek.

Castillo said he didn’t know whether the stretch of UP track through Niles Canyon has suffered mudslides over the years. All UP tracks in California are subject to a “very robust” inspection process, and the tracks had gone through an additional “stormwatch” inspection just ahead of this weekend’s rainstorms, he said.

“It’s impossible to know when mudslides are going to happen,” he said.

California Fish and Wildlife is monitoring Alameda Creek for possible oil spills or affected wildlife, but the impact of the derailment appears to be minimal, said Steve Gonzalez, agency spokesman. The train uses air brakes rather than hydraulic, which reduces the risk, he said.

As a precaution, professional oil spill responders set up a barrier of absorbent material downstream Monday night to catch any possible spill.

The workers also strung a rope across Alameda Creek to pull a boom across in case there is any oil sheening from the wreckage. More spill response equipment was placed at a staging area, he said.

“They’re not going to take any chances,” Gonzalez said.

On Monday night, the first train car was partially submerged in water as crews frantically worked to rescue those inside, Alameda County Sheriff’s Office spokesman Sgt. J.D. Nelson said.

Kathy Heilmann of Livermore was in a middle car when the train derailed.

“I screamed,” she said. “Once I realized I wasn’t in danger I was more calm. I heard people saying they saw the conductor come out of the water sopping wet and it looked like blood was gushing from his head.”

Many passengers climbed out through the emergency windows. Arun Soman, 38, of Pleasanton, saw the car in front of him hanging off the tracks as well the one submerged.

“We saw people going in and rescuing people,” he said, “We heard two or three people were stuck but they got everyone out.”

“We all stuck together and helped each other out,” said Ashley Fultz who was returning from to Stockton from her job at Stanford Hospital.

From 2010 to 2014, 318 train derailments occurred in California, according to data from the state Public Utilities Commission, which regulates all railroads in the state. Nearly all of those derailments involved freight trains, records show. An exact breakdown by railroad was not immediately available.

Check back for updates.

David Early, Matthias Gafni, Julia Prodis Sulek, Rebecca Parr, Sam Richards, Thomas Peele, Jason Green, Rick Hurd and George Kelly contributed to this report. Contact Mark Gomez at 408-920-5869 and follow him at Twitter.com/MarkMgomez.

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