Pennsylvania’s unprecedented pandemic election went ‘remarkably smoothly.’ Now all that’s left is counting votes.

Despite a deadly pandemic, massive changes to the electoral system, and misinformation-driven fears of chaos — many of them fueled by the president of the United States — Election Day in Pennsylvania was almost like any other.

There were busy polling places, long lines, and occasional mishaps, especially in the always-bumpy early hours of the morning. But with the nation watching, Pennsylvania saw a largely smooth process in its first election with mass mail voting.

Several lawsuits were filed by Republicans challenging certain aspects of the state’s election guidance, and a challenge to the counting of mail ballots received through Friday remained before the U.S. Supreme Court. But across the populous Philadelphia region, no major problems had been reported by Tuesday night.

It was the culmination of weeks of mail voting, a new form of early in-person voting, and preparations to accommodate people at traditional polling places as a new wave of coronavirus infections was cresting.

The stakes had been raised by baseless attacks from President Donald Trump on mail ballots generally — and Pennsylvania’s election, specifically — as being fraudulent. The pandemic caused people to don masks and sanitize their hands. But turnout for in-person voting appeared robust.

“Today’s election in the commonwealth went remarkably smoothly,” Pennsylvania Secretary of State Kathy Boockvar said. “We have no major or widespread events to report.”

With the casting of votes completed at the end of the day Tuesday, the focus shifted to the next phase: counting the ballots. With elections officials expecting to work all night Tuesday into Wednesday, that effort was set to continue around the clock and through the rest of the week.

Officials reminded Pennsylvanians that counting would take time and urged patience.

“What’s most important is that we have accurate results and that every vote is counted, even if that takes a little longer,” Gov. Tom Wolf said.

“We’re doing everything we can to make it as early as possible,” said Lisa Deeley, chair of the Philadelphia City Commissioners. She said that the work would be done 24 hours a day until it was completed.

Reports of problems at polling places appeared no more frequent than usual. In Philadelphia — which Trump put in the national spotlight when he said that “bad things happen” in the city — officials reported mostly ordinary election incidents, only a few of which remained under investigation by the end of the day. Some sites experienced minor or moderate complaints, such as broken voting machines or campaigning too close to polling places.

» READ MORE: It may look like Trump is winning Pa. before votes start to shift toward Biden. Whoever wins, that’s not fraud.

The state did not receive any reports of violence at polling places, though “a few” accounts of voters feeling intimidated were resolved by elections officials, Boockvar said. As the counties worked Tuesday night to tally and report results, the state did not have an estimate for total turnout or for the number of mail ballots that might need to be disqualified because of flaws.

“For an election that had as many passions as this election seems to have had, the issues … are really run-of-the-mill issues that we’ve had pretty much every election,” Wolf said.

Perhaps the biggest source of confusion, reported in multiple counties, was the voters who had requested mail ballots but still went to the polls, where they had to surrender their mail ballots or submit provisional paper ones in a process that sometimes slowed lines. And while officials had braced for misinformation and the possibility of voter intimidation, the resilience of voters and relative calm appeared to carry the day.

A few polling places in the Philadelphia suburbs had such high turnout that voters waited in line for hours. And as the lines snaked, county officials behind the scenes were already starting to count the 2.5 million mail ballots that had been received.

“There was a lot of uneasiness and anxiety coming into the election, but overall voter experiences have been generally positive,” said Thi Lam, operations director for SEAMAAC, a nonprofit that supports immigrants and refugees and had about 200 volunteers at polling places across South Philadelphia. The only issues centered on poll workers requiring voters to present ID against state election law, he said: “There’s been no major intimidation, just a little misinformation.”

The way Pennsylvania ran its election came under the national spotlight in part due to Trump, who on Monday claimed that counting mail ballots, which are eligible as long as they arrive at county elections offices by Friday evening, will “induce violence on the streets.”

That heightened the already challenging task of pulling off the most complex election that Pennsylvania officials have run. This is the first year any Pennsylvania voter can vote by mail, expanding the state’s restrictive absentee system and forcing 67 counties to essentially run two elections at once: one by mail and one in person.

In one year, the counties built new vote-by-mail systems, as the pandemic drove massive demand for mail ballots and created a logistical nightmare for in-person polls.

Lackawanna County had gotten back most mail ballots, a spokesman said, and a Montgomery County official said the counting was “humming along” with workers “in good spirits.”

“It really is like an assembly line,” said Julie Wheeler, president commissioner in York County, where about 100 employees counted mail ballots inside a large exhibition center at the county fairgrounds.

Just 17.5% of mail ballots sent to Pennsylvania voters had not been returned by Tuesday afternoon, the state said. But many of those voters showed up at their polling places to hand over the unused mail ballot and vote in person, county officials reported. That process caused confusion in some areas, and Philadelphia elections commissioners fielded questions about the process all day.

Brian Marsh, 41, said poll workers incorrectly had him fill out a provisional ballot instead of voting by machine when he turned over his mail ballot at his Philadelphia polling place.

“Procedurally, that’s not correct,” said Al Schmidt, a Republican and one of the three city commissioners who run Philadelphia elections. “But at the end of the day, it is an eligible voter casting a vote that will count. No one is disenfranchised.”

At polling places in Bucks County, officials had to print more of the affidavits required for voters to sign when turning over the mail ballots, said county commissioner Bob Harvie. Those affidavits were also reported to be running low at polling places in Philadelphia, said David Thornburgh, CEO of the Committee of Seventy.

State elections officials had expected some voters to request mail ballots but show up in person, and counties have various procedures in place to catch any potential double-votes.

Some confusion also remained over the state Republican Party’s bid to reverse the Pennsylvania Supreme Court’s decision that mail ballots can be received by county elections offices until 5 p.m. Friday. Because the GOP’s case remains before the U.S. Supreme Court, ballots arriving under that deadline will be counted separately from earlier ballots.

In Lancaster County, a county commissioner suggested on Facebook that the county wouldn’t open or count mail ballots that arrive after the polls close until the U.S. Supreme Court rules on the case. That prompted the county solicitor to confirm that the county would, in fact, process mail ballots that arrive before the Friday deadline.

Citing too few staff members to count mail ballots while also running an in-person election, some counties, including Beaver, Montour, and Mercer, said they wouldn’t begin counting mail ballots until Wednesday.

In York County, a spokesperson estimated that the county had received several hundred “naked ballots” — ones mailed without secrecy envelopes, which cannot be counted. Officials there and in Erie County said some efforts were being made to open the envelopes and contact the senders so they could vote in person before the polls closed.

The state’s guidance allowing that type of contact with voters prompted another lawsuit against Pennsylvania’s election process. Lawyers for Pennsylvania Republicans filed suit Tuesday night seeking to set aside all mail-in ballots by voters who were given the chance to correct possible mistakes. Boockvar said the state disputes the claim.

It will take days for all votes to be counted. Some voters said they were glad to know mail ballots would be counted, while others said they had voted in person because they were wary of mail voting or repeated Trump’s claims about possible fraud.

One two-time Trump voter, Lackawanna County resident Tom Stec, 61, dismissed the state’s expansion of mail voting this year as nonsense.

“I’m thinking there will be forgeries, scams,” he said. “I don’t trust it. … Our government, we don’t do things well.”

In contrast, Laura Pavlecic, 54, volunteering at a polling place in Richland Township in Bucks County, saw Trump’s call for Pennsylvania to stop counting mail ballots Tuesday night as “a huge scare tactic” and “voter intimidation.”

And Noah Inghram, 20, a student from Moon Township in Allegheny County, said what was important was for all to have a voice.

"All votes should be counted,” said Inghram, who voted for Trump. “I think it’s important that everyone gets a say in this election.”

Staff writers Ellie Silverman, Ellie Rushing, Samantha Melamed, Allison Steele Jessica, Calefati, Chris Palmer and Jeremy Roebuck, Vinny Vella, and Sean Collins Walsh contributed to this article, along with the staff of The Inquirer and Angela Couloumbis and Ed Mahon of Spotlight PA, along with Marie Albiges and Tom Lisi for Spotlight PA and Votebeat.