Long Island Rail Road commuters endured another difficult morning Wednesday, as nearly every branch experienced delays and cancellations tied to lingering effects of the recent winter storm.

According to the MTA, all but two LIRR branches were affected during the morning rush, primarily due to weather-related switch problems, equipment shortages, and a small fire west of Jamaica that further disrupted service.

Some riders reported being significantly late. One passenger said his train arrived at Penn Station nearly an hour behind schedule.

LIRR President Rob Free said extreme cold temperatures were largely to blame, noting that the system has been operating in persistent sub-freezing — and at times sub-zero — conditions.

“We’re trapped in extremely cold weather which has been persistent,” Free said. “Not only sub-freezing, but sub-zero temperatures. On any system, that would create issues.”

Despite rider frustration, Free said most service has continued to operate. He reported that more than 97% of scheduled trips were completed on Tuesday.

At the Mineola station, News 12 observed workers manually heating switches using natural gas burners in an effort to keep trains moving. Crews are expected to remain deployed throughout the week to clear snow, with some areas of the system seeing totals of up to 15 inches.

When asked when commuters could expect a normal rush hour, Free said service has been operating as expected given the conditions.

“I think today was normal, in terms of this storm,” he said.

Some riders acknowledged the challenge facing railroad crews. “They do a pretty good job clearing stuff off,” said passenger Will Gropper. “It’s a crazy operation to get rid of that much snow.”

Free emphasized that safety remains the top priority.

“We got people where they needed to go safely, and that’s what matters the most,” he said.