lori jordan set up a makeshift office at the south station. >> it's always something. >> reporter: because boarding a train from here was not going to happen any time soon. >> i took the red and orange and. >> now it's something else. >> reporter: this morning, amtrak announced the signal system at tower one had failed. making it impossible for commuter rail trains to safely travel to south station a spokesperson for keolis who runs the commuter rain explains. >> it's just like a traffic signaling system or air traffic control system. it tells you whether it's okay along the tracks. when this system guess out it has a enormous impact. >> reporter: after a hectic morning with commuters forced to deboard before south station to stapped in long lines and -- stand in long lines and make unexpected connections amtrak crews were on the tracks trying to fix the issue and using manual signals holding up signs to direct limited trains slowly. >> to have this happen and to find out about it, at 6 in the morning, and to be scrambling trying to figure out how to help people deal with the morning commu