An assault suspect who barricaded himself in a San Rafael hotel room was found dead Thursday of an apparent self-inflicted gunshot wound, police said.

The man was identified as Peter James Thomas, 38, who was suspected of slashing several employees with a knife during a shoplifting incident Sunday at United Markets in San Rafael. His last communication with police was late Wednesday night.

Thomas's girlfriend, previously reported to be in his second-floor room at the Extended Stay Deluxe Hotel, was actually in a different room on the fourth floor, police said.

Although Thomas told police his girlfriend was with him, police developed information that she was not in Thomas's room and located her and the couple's dog around 8 a.m. Thursday. It was unclear why she did not come forward during the 24-hour standoff, when the hotel was swarmed with police and news media.

Around 12:30 p.m. Thursday, police drilled a hole in the wall of Thomas's room and inserted a camera. Investigators saw the body and broke into the room.

An autopsy was pending.

Police did not release the name of Thomas's girlfriend.

In addition to the knifing incident, Thomas had been wanted since January 2010 on a $70,000 warrant for failing to appear in court in a Mill Valley drug and weapons case. He was charged with burglarizing the Mill Valley Health Club, being a felon in possession of a gun and ammunition, and possessing methadone, metal knuckles, identity theft materials and methamphetamine.

The standoff began Wednesday morning after police learned the United Markets knifing suspect was staying at the hotel. Thomas barricaded himself in the second-floor room and fired a gunshot out the window toward traffic on Interstate 580.

Authorities briefly shut down the Richmond-San Rafael Bridge, evacuated about 40 hotel guests but not the whole building, and closed Interstate 580 between the bridge and Highway 101 to prevent Thomas from shooting at traffic.

The freeway closure — which continued all day and into the night while police negotiated with Thomas — forced traffic to side streets and gridlocked traffic on San Rafael side streets, Highway 101 and Sir Francis Drake Boulevard.

The highway section was not reopened until 12:40 a.m. Thursday, when police got a large crane and installed a 1-inch-thick metal plate in front of Thomas's window.

The costs of the operation — in police overtime, losses to local businesses and other expenses — will take several days to estimate, said San Rafael City Manager Nancy Mackle.

In addition to the response by the San Rafael Police Department, dozens of officers, sheriff's deputies and law enforcement agents provided assistance.

Court records list Thomas as a San Francisco resident. According to the California Department of Corrections and Rehabilitation, Thomas served time for numerous convictions in San Francisco, including second-degree robbery in 1993 and 2002 and vehicle theft in 1999.

His prison history includes stints in San Quentin, Solano and Avenal, and he escaped from a prison firefighting camp in 1996, according to prison records.

The extended road closure and ensuing traffic jam had some drivers fuming more than their overheated engines. Thomas Harbinson, a lawyer who lives in Ross, said it took him three hours to get home from San Francisco on Wednesday.

"It seems to me (police) could have done something but sitting there for 10 hours and then he's dead anyway," he said. "I think they should have done something, either break in or funnel some gas in there."

As for the possibility that a woman was being held hostage in the room, Harbinson said it should not have been a deterrent.

"We can't let someone use that as a basis for doing nothing," he said. "They could gas her too."

"Breaking the window or door and throwing in tear gas would have done the trick without 2 days of insanity here on the freeways," San Rafael resident Marcia Blackman said in an email.

Capt. Amy Mangan, commander of the California Highway Patrol office in Marin, said the decision to close the freeway "was not one taken lightly."

"The CHP instituted a traffic management plan, which included the use of all available resources and personnel, the Transportation Management Center, changeable message signs, Caltrans, as well as information feeds to the media so the public could stay abreast of the situation and plan accordingly," she said in a statement. "There was not one moment during the incident that wasn't spent trying to develop solutions to address the possible gunfire toward the freeway, and we're very pleased with the concept and the coordination regarding the placement of steel plates over the windows to ensure the safety of all those on scene and the motoring public.

"In addition to the above, the CHP and Caltrans deployed officers and personnel across the impacted portion of Marin to facilitate and expedite flow of traffic. The CHP had 100% support from San Rafael Police Department to implement our traffic plan in the interest of public safety."

Contact Gary Klien via email at gklien@marinij.com