The LIRR said it is operating on or close to schedule during Tuesday’s morning commute after earlier signal trouble in an East River tunnel caused systemwide congestion.

From about 8 to 9:15 a.m. the Long Island Rail Road experienced delays, cancellations and congestion because of the signal trouble.

Some trains were canceled at Jamaica, or diverted to Hunterspoint Avenue or Atlantic Terminal, the LIRR said.

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And for a while, NYC Transit honored LIRR fares.

Most of the congestion was projected to be on the Babylon, West Hempstead and Far Rockaway branches, an LIRR spokeswoman said shortly after the alerts announcing the signal trouble.