The House Armed Services Committee passed its sweeping Defense authorization early Thursday morning, authorizing $638 billion in Defense spending.

The Pentagon policy bill includes stripping commanders’ ability to overturn guilty verdicts to deal with a rise in military sexual assaults, a prohibition on transferring Guantánamo detainees to the United States and a rejection of new base closures.

The committee passed its authorization bill on a 59-2 vote after a 16-hour markup, which began Wednesday morning and lasted until 2:14 a.m. Thursday. The bill will be debated on the House floor next week.

Reps. Jackie Speier (D-Calif.) and John Garamendi (D-Calif.) were the only committee members to vote against the final legislation.

{mosads}The bill provides an increase of $5.1 billion for the war in Afghanistan from the Pentagon request, and it sets base Pentagon spending at $526.6 billion, the same amount that was requested in President Obama’s budget.

That funding level is $52.2 billion over the budget caps set by sequestration, however, a topic that was debated only sparingly on Wednesday.

Because the panel’s bill was over the budget caps — as are the Senate and Obama administration budgets — the Pentagon could be facing another across-the-board cut in 2014 if sequester is not averted.

“I think in this committee, there’s a growing awareness that sequestration is a fact of life, so whatever we do here today will wind up being reduced by a significant amount,” said Rep. Adam Smith (D-Wash.), the top Democrat on the committee.

After 1 a.m. Thursday, the committee debated a measure from Rep. Jim Cooper (D-Tenn.) to give the Pentagon $20 billion in flexibility to transfer funds between accounts, up from $3.5 billion granted in the authorization bill.

Pentagon officials have warned that the military is facing shortfalls in its operations and maintenance accounts, and they’ve said flexibility could help alleviate the problem to some degree.

“This is insanity, and so far, this committee has not done anything about it,” Cooper said. “I’m not saying this is a perfect solution, but it is a start … I am sorry it is one in the morning before we face the elephant in the room.”

The amendment failed, however, on a 16-45 vote, and was opposed by both Armed Services Chairman Buck McKeon (R-Calif.) and Smith.

“What you’re asking is to give full discretion for $20 billion. That really doesn’t solve the problem,” McKeon said. “What we really need to do is get rid of the sequestration.”

As the Pentagon faces tightened budgets, Smith criticized the committee for rejecting several cost-cutting measures that the Pentagon had requested, including a new round of base closures and new healthcare fees.

“I don’t think this committee has the luxury to be so parochial,” Smith said.

He was clearly in the minority, however, as the committee rejected his amendment 44 to 18 to reverse a restriction on Pentagon planning for future base closures.

Smith also fought a losing battle to lift a restriction on transferring detainees from Guantánamo onto U.S. soil, which has been included in the past several Defense authorization bills. The prohibition is a key roadblock to President Obama’s new push to close the detention facility.

Just as the full House passed a restriction on building U.S. facilities in the military construction appropriations bill, the committee rejected Smith’s amendment on a 23-38 vote.

The panel did not get into a major debate on military sexual assault Wednesday, but the bill included significant changes to the military’s judicial code in order to deal with sexual assault.

The panel included legislation from Reps. Michael Turner (R-Ohio) and Niki Tsongas (D-Mass.) that stripped military commanders’ authority to overturn guilty verdicts in a post-trial review.

The adopted measure also established a mandatory sentence of dismissal or dishonorable discharge for service members who were convicted of sexual assault.

There has been a major push in Congress to tackle sexual assault in the military on the heels of a Pentagon report estimating 26,000 assaults last year, up from 19,000 in 2010.

The committee’s markup did not address proposals to make larger changes to the military’s judicial code, including one from Speier to take sexual assault cases outside the chain of command.

Speier told The Hill on Wednesday that she was working with Republicans to get a vote on her amendment when the authorization bill goes to the floor next week.

Top military leaders expressed uniform opposition to taking cases outside the chain of command during a Senate hearing on Tuesday.

The most partisan debate in the committee Wednesday focused on missile defense issues, in particular Republican plans to build a new East Coast missile site by 2018.

The committee passed an amendment from Turner to direct $140 million for construction on the site by a 33-27 vote.

“It is imperative that we move quickly to ensure that our missile-defense system is expanded and it is completed,” Turner said.

Democrats argued that the technology is not yet ready, and it would be premature to begin building a new site.

“This is too much money, too early to be helpful to the security of the American people,” said Cooper, the ranking member of the Strategic Forces subcommittee.

The Republicans on the panel also tangled with Democrats over the Pentagon’s biofuels program, a frequent target of GOP lawmakers for cuts.

The committee pushed back on a number of weapons programs that the Pentagon wanted to retire, including the Global Hawk Block 30 drone and seven cruisers and two amphibious warships.

Democrats also expressed concerns about the potential for discrimination against gay service members after the committee expanded a “conscience clause” for military chaplains in last year’s bill. The amendment from Rep. John Fleming (R-La.) stated that the military had to accommodate service members’ actions and speech, in addition to beliefs, which was the current language.

The Senate Armed Services Committee will be marking up its version of the Defense authorization bill in closed session next week.

— Carlo Muñoz contributed.