I do not know at what you are looking in the CAEPIPE or AUTOPIPE output.
A mode shape is just that, a shape that the system may take under no load. You do this by solving Ma+Kx=0. Given that response is harmonic, then let x=A*sin(wt). Acceleration is second derivative with respect to time of x, or a=-(w^2)A*sin(wt), or a=-(w^2)x.
Ma+Kx=M*[-(w^2)x]+Kx=0
[K-(w^2)M]x=0
So either [K-(w^2)M]=0 or x=0. The interesting solution is [K-(w^2)M]=0. The (w^2)'s are the eigenvalues that satisfy this relationship. The natural frequencies are those w's divided by 2*pi. For each of these eigenvalues there is a matching distorted shape of the system that can be achieved with no load. These mode shapes have no defined magnitude, only a relative position with respect to all other nodes, as no load was needed to set these positions. When you apply transient loads, each mode will influence the total transient response of the system - that is modal analysis.