Update: Is it all clear now? Muni claims everything's back to normal.

Speaking of Muni, SF Appeal warns that there are serious delays reported on the inbound N Judah and J Church lines. The underground trains have been replaced by shuttle buses running from Church and Duboce, down Market, to Embarcadero.

Muni confirmed that they're having problems with the ATCS (automatic train control system).

As it usually goes in these cases, the Church and Market transit areas are currently in total chaos.