Many airlines were forced to cancel flights due to the weather, but Southwest was the most affected. About 4,000 domestic U.S. flights were canceled Monday, according to the tracking website FlightAware, and 2,900 of those were Southwest’s. Nearly 2,500 more flights had already been canceled as of 5 a.m. Tuesday and problems are likely to continue at least into Wednesday.

Southwest spokesman Jay McVay said at a press conference in Houston that cancellations snowballed as storm systems moved across the country, leaving flight crews and planes out of place

“So we’ve been chasing our tails, trying to catch up and get back to normal safely, which is our number one priority as quickly as we could,” he said. “And that’s exactly how we ended up where we are today.”

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Passengers stood in long lines trying to rebook their flights. The Department of Transportation said on Twitter that it was “concerned by Southwest’s unacceptable rate of cancellations and delays & reports of lack of prompt customer service.” The tweet said the department would look into whether Southwest could have done anything about the cancellations and whether the airline was complying with its customer service plan.

Southwest CEO Bob Jordan told The Wall Street Journal in an interview that the airline would operate just over a third of its usual schedule to allow crews to get back to where they needed to be.

“We had a tough day today. In all likelihood we’ll have another tough day tomorrow as we work our way out of this,” he said Monday evening. “This is the largest scale event that I’ve ever seen.”