Commuters attempting to travel through the New York metropolitan area are in for a rude awakening as Friday afternoon’s rush hour begins.

The Long Island Rail Road, NJ Transit and Amtrak are still operating on limited service as a transit meltdown set off by a Thursday morning fire in an East River tunnel drags on.

NJ Transit said its Midtown direct service will be diverted to the Hoboken terminal for the rest of Friday. LIRR said most of its trains will be rerouted to Grand Central or Atlantic Terminal, with no westbound service to Penn Station, while Amtrak continues to warn travelers of significant delays. LIRR also said the rerouted trains wouldn’t be reflected in its app, and urged travelers to listen for announcements.

The disruptions come as LIRR prepares its riders for a potential service shutdown starting at midnight. Unions representing LIRR workers are threatening to strike after reaching a stalemate with the MTA over pay raises and work rules.

The Thursday fire broke out in a tunnel connecting the LIRR between Manhattan and Queens. Officials with Amtrak, which owns the tunnel, said the cause of the fire was still under investigation as of Friday afternoon. They did not specify what equipment in the tunnel was damaged, or provide a timeline of when it will be repaired.

It took more than an hour to extinguish the fire, which led to a cascade of service delays that also backed up Amtrak’s own Northeast Corridor service. Amtrak warned Friday its trains heading through the New York area could see delays of about 40 minutes.

This is a developing story and may be updated.