Deputy Attorney General Sally Q. Yates at the Justice Department on May 15, 2015. Yates made recommendations on clemency for federal inmates to President Obama. (Evelyn Hockstein/For The Washington Post)

Justice Department officials have completed their review of more than 16,000 clemency petitions filed by federal prisoners over the past two years and sent their last recommendations to President Obama, who is set to grant hundreds more commutations to nonviolent drug offenders during his final days in office.

“Everyone has killed themselves here to get the final recommendations to the president,” Deputy Attorney General Sally Q. Yates said in an interview. “We were in overdrive. We were determined to live up to our commitment. It was 24-7 over the Christmas break.”

U.S. Pardon Attorney Robert A. Zauzmer has not taken a day off since Yates brought him on in February 2016 to sift through the backlog of thousands of petitions. From her home in Atlanta, Yates said she reviewed hundreds of petitions during the holidays.

[Struggling to fix a ‘broken’ system: How Obama began to unwind the drug war]

As President-elect Donald Trump prepares to take office, Justice officials worry that his administration will dismantle Obama’s clemency initiative, which has resulted in the early release of 1,176 drug offenders who were sentenced under the severe mandatory minimum laws passed in the 1980s and 1990s during the nation’s “war on drugs.” More than 400 were serving life sentences. Yates said Obama will grant “a significant” number of commutations this week, but would not specify a number. Several people close to the process said it will be several hundred.

Those officials also fear that the next attorney general may undo new criminal justice policies. Then-Attorney General Eric H. Holder Jr. put in place a policy three years ago to reserve the most severe drug-offense penalties for high-level or violent drug traffickers — and no longer charge low-level, nonviolent drug offenders with crimes that impose severe mandatory minimum sentences. Justice Department data indicate that prosecutors are now focusing on more-serious drug cases, and there have been fewer charges that carry mandatory sentences.

Neither Trump nor his attorney general-nominee, Sen. Jeff Sessions (R-Ala.), has said what actions might be taken on drug charging policy or clemency, but during his campaign, Trump criticized Obama’s initiative to grant commutations.

“Some of these people are bad dudes,” he said. “And these are people who are out, they’re walking the streets. Sleep tight, folks.”

Yates, who has been responsible for the day-to-day running of the 113,000-employee Justice Department, led the clemency initiative alongside other criminal justice reform efforts. In November, for instance, she created a semiautonomous “school district” for inmates in federal prison. With its own superintendent, the school district offers programs for literacy, high school diplomas and postsecondary education.

She cited research that shows that inmates participating in correctional education programs are 43 percent less likely to reoffend and return to prison than those who do not participate; the initiative could mean cost savings for the Federal Bureau of Prisons. Federal prison costs represent about one-third of the Justice Department’s $27 billion annual budget.

Last year, Yates also oversaw the effort to mandate new standards for privately run halfway houses and directed the Bureau of Prisons to work to end its use of private prisons to house federal inmates. It is unclear whether these initiatives will remain in place, especially given that Trump has praised private prisons.

“I do think we can do a lot of privatizations and private prisons. It seems to work a lot better,” Trump said last year. Hours after his election victory, the stock prices of the two largest private-prison companies soared.

Yates pushed hard for sentencing reform legislation in Congress, giving speeches and meeting with Republican lawmakers on Capitol Hill. The effort had a broad coalition of bipartisan support, including from the NAACP, the conservative Koch brothers, and lawmakers including Sens. Mike Lee (R-Utah) and Cory Booker (D-N.J.).

But the legislation, which would have reduced federal mandatory minimum sentences for drug and gun crimes, making the reductions retroactive for some inmates, went nowhere because of disagreement among Senate Republicans.

“I am really disappointed,” Yates said. “We had this moment in time where we had Democrats and Republicans, conservatives and liberals and all sorts of interest groups. We even had the votes in the Senate but couldn’t get it to the floor. ”

At several points during the past two years, it appeared that Obama’s clemency initiative might have been derailed, partly by a lack of resources but also by a cumbersome review process.

After Holder and then-Deputy Attorney General James Cole began the effort in the spring of 2014, thousands of inmates applied. To help them with their petitions, outside lawyers formed an organization called Clemency Project 2014, which includes Families Against Mandatory Minimums, the American Civil Liberties Union, the American Bar Association and the National Association of Criminal Defense Lawyers.

About 4,000 volunteer lawyers signed up to help in what has become one of the largest pro bono efforts in the history of the legal profession in the United States. Once the lawyers submitted the petitions, the U.S. pardon attorney made recommendations to the deputy attorney general, who reviewed the cases and sent them to the White House counsel, who also reviewed them before choosing which ones went to Obama.

When Yates arrived at Justice in the spring of 2015, the clemency program was overwhelmed and bogged down. Advocates criticized the inefficient process and urged the Obama administration to pick up the pace for the inmates waiting for relief from unfair sentences.

“There wasn’t an apparatus set up,” Yates said. “When I arrived, they were doing the best they could . . . but we didn’t really have a playbook.”

Early last year, more than 9,000 clemency petitions were pending, and the pardon attorney at the time was so frustrated that she quit.

Yates brought on Zauzmer, a longtime federal prosecutor, who prioritized applications so that Justice lawyers could focus on inmates who met the criteria: Inmates had to have served at least 10 years; had no significant criminal history; no connection to gangs, cartels or organized crime; and probably would have received a “substantially lower sentence” if convicted today.

“These are big decisions that you’re making,” Yates said, alluding to the public-safety risks and the need to provide a “sophisticated analysis” to the president.

“If it’s to let someone out of prison early, earlier than what their original sentence was, you’ve got to be careful about those decisions,” she said. “There’s lots of people whose current offense or conviction is a nonviolent drug offense . . . but you have to look at their past as well and at their criminal history. You have to look at their conduct [in prison].”

Not all inmates who have been granted clemency will be released immediately or even in a number of months. Last summer, the Obama administration began granting clemency to some inmates by reducing their sentences; in some cases, they will remain in prison for years.

At the end of August, Yates announced that she would review and give Obama a recommendation on every petition from a drug offender that was still in the department’s possession at that time — about 6,195 petitions. She did that, and included several hundred petitions received through Sept. 15, after her cutoff date. She also reviewed petitions that came in as late as Nov. 30 from drug offenders serving life sentences. By last Friday, the final number of petitions reviewed was 16,776.

“Sally deserves a lot of credit,” Holder said in an interview. “She set this goal of looking at every drug-clemency petition, and they accomplished that.”

The inmates whose names are on those clemency petitions “are in a dark place, and the hope of clemency is the only light they have,” said Sharanda Jones, 49, who received a commutation from Obama in December 2015 after serving nearly 17 years of a mandatory life sentence for her first conviction, a nonviolent drug offense.

“Clemency from President Obama literally saved my life,” said Jones, who now lives in Dallas near her 25-year-old daughter and 7-month-old granddaughter. “I could never thank him enough for the priceless gift of freedom, but I hope that my actions and the positive way I live my life show him the depths of my gratitude.”