Metra said the issues began with the Canadian National Freight Rail System's Positive Train Control. This is the system that controls the trains that may move too fast, and can override the engineers.
Metra said CN has restored its computer systems, and Metra rail service with its Milwaukee North, North Central Service and UP Northwest has been restored. Heritage Corridor was canceled for the morning.
Metra said it expects normal service for the evening commute, and was moving more trains and equipment downtown to prepare.
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A number of commuters said they didn't really know what to expect or how to plan Monday morning.
"It's frustrating because it's a letdown for sure," Metra passenger Froylan Arellano said. "I have places to be, and I would rather just be on my way, but now I am here just waiting."
"Oh my God it was very hectic actually waiting on the train; on the actual ramp, it was like a very long time, used to being here on time," commuter Martell Wilburn said. "I'm late for a meeting right now; it's just ridiculous."
Some Metra passengers made it into the city. Others were left waiting at suburban train stations, including Arlington Heights.
"Well, I didn't know anything. I just see on my Ventra app that it's going to be 35 minutes late, and it keeps getting postponed," Metra passenger Jacob Prawica said.
"It was horrible; normally, I take the 7:30 train. It didn't get there 'til about 8:30 today, so an hour late to work," Metra passenger Michael Freeman said.
"It makes me feel lost, kind of makes me feel like I don't know what's going on. It's kind of upsetting," Metra passenger Katie Ericson said.
In a statement, CN said, "Earlier this morning, an IT issue impacted CN's train dispatching system in the US, including Metra and Amtrak trains. The issue has been resolved and trains have resumed their safe movements."
A handful of Amtrak trains were canceled between Chicago and St. Louis and Chicago and Carbondale, stemming from the issue with CN.
CN operates nearly 19,000 miles of railway across North America, connecting the Atlantic, Pacific and Gulf coasts. Some Metra trains run on CN tracks.