The White House on Thursday stood by its characterization of a covert counter-terrorism operation in Yemen as a success, a day after after the Pentagon concluded that civilians were likely killed and President Trump honored the Navy SEAL gunned down in the assault.

"It's hard to ever call something a complete success, when you have the loss of life or people injured," White House Press Secretary Sean Spicer said. Chief Special Warfare Operator William "Ryan" Owens, 36, was the first known combat fatality of Trump's presidency.

"But I think when you look at the totality of what was gained to prevent the future loss of life ... it is a successful operation by all standards," Spicer added. 

President Trump’s nominee to run the Environmental Protection Agency survived a rancorous committee vote Thursday, putting him on the path to full Senate confirmation and a confrontation with California.

Scott Pruitt, who oil and gas companies are betting will help them reassert dominance over the energy economy, has cast doubt on California’s power to force automakers to build more efficient, cleaner-burning cars.

But he soon may learn that battles like the one he appears poised to launch can be full of unpleasant surprises.

Secretary of State Rex Tillerson marked his first day of work Thursday by acknowledging turmoil in the department he will lead and urging anxious employees "not to let personal convictions overwhelm our work on one team."

He stepped into the grand lobby at the State Department, flanked by dozens of national flags and hundreds of  employees, and invoked a folksy humor and calm manner, even though his message was firm.

"Hi. I'm the new guy," he told the crowd in a Texas drawl.

Republicans voted to send to the full Senate the nomination of President Donald Trump's pick to lead the Environmental Protection Agency on Thursday.

The vote came after Republican suspended committee rules to muscle through the vote, because Democrats boycotted the meeting.

Seats reserved for the 10 Democrats on the Senate Environment and Public Works Committee were empty Thursday as the meeting to advance the nomination of Scott Pruitt was gaveled to order. Accusing the absent Democrats of obstruction, the remaining 11 Republicans voted unanimously to suspend rules requiring at least two members of the minority party to be present for a vote to be held.

President Trump seemed to acknowledge a recent string of "tough" phone calls to foreign allies, saying at the National Prayer Breakfast on Thursday that they were part of what he characterized as an effort to straighten out a troubled world.

"Believe me when you hear about the tough phone calls I'm having, don't worry about it," Trump said.

The comments came after the White House and the Mexican government denied reports by the Associated Press and Mexican media that he threatened to send U.S. troops to Mexico to fight "bad hombres" during a call with President Enrique Peña Nieto.

President Trump suggested in an early morning tweet that that federal funds could be taken from UC Berkeley after violent protests caused school officials to halt a planned speech by conservative firebrand Milo Yiannopoulos.

University officials called off the event about two hours before Yiannopoulos was to speak at the student union, where more than 1,500 people had gathered outside. Some hurled metal barricades and others smashed windows.

“This is not a proud night for this campus, the home of the free-speech movement,” said Dan Mogulof, a Berkeley spokesman.

The Mexican government on Wednesday vehemently denied reports that President Trump threatened to send American soldiers into Mexico during a phone call with Mexican President Enrique Peña Nieto.

Such a threat “did not happen during that call,” said a government statement released on Twitter on Wednesday night.

"I know it with absolute certainty there was no threat,” Peña Nieto spokesman Eduardo Sanchez said in a radio interview. “The things that have been said are nonsense and a downright lie."

Civilians, including children, were probably killed in Yemen on Sunday during a predawn special operations raid, U.S. military investigators have determined, an assault in which a decorated Navy SEAL commando also died.

The raid was the first known counter-terrorism operation and first confirmed combat fatality under President Trump.

U.S. Central Command, which oversees military operations in the Middle East, said in a statement late Wednesday that an unspecified number of civilians were probably killed in the midst of a fierce battle that included gunfire, hand grenades and airstrikes.

The U.S. has put Iran “on notice” for carrying out a medium-range ballistic missile test and attacks by proxy forces on a Saudi frigate, White House National Security Advisor Michael Flynn said Wednesday, a cryptic comment that appeared to signal the Trump administration is taking a tougher stance on Iran than its predecessor.

“The Trump administration condemns such actions by Iran that undermine security, prosperity, and stability throughout and beyond the Middle East and place American lives at risk,” Flynn told reporters at the White House.

Iran’s first real test of the Trump administration came Sunday, when the U.S. military tracked an Iranian missile launch at a site more than 130 miles east of Tehran.  

The Trump administration has clarified language in its travel ban affecting seven majority-Muslim countries to make clear that green card holders from those countries do not need to get a waiver before entering the U.S., the White House said Wednesday.

White House spokesman Sean Spicer announced the change during a briefing with reporters, saying it was made in the name of efficiency.  

"They no longer need a waiver because if they are a legal permanent resident, they won't need it anymore," Spicer said.