There are many phrases that go with it, such as 'Pitch Runner', which is describing when you skip a base, and Homer, which is going straight to fourth base, or sex. Run out means being stopped before getting to a base.
Obviously, there is some discrepancy, like blowjobs and handjobs obviously coming in somewhere between third and fourth.
Person 2: Err...well, we-
Person 1: Baseball System, man.
Person 2: (quietly) ran out before first.