We use self-consistent field theory to investigate the directed self-assembly of cylinder-forming block copolymers for the purpose of a graphoepitaxial pitch multiplication. We focus in particular on conditions where two minor-block cylinders form inside confining rounded templates with neutral sidewalls and substrates. In addition to perfect cylinders, various defective morphologies can also self-assemble in the guiding templates. According to SCFT simulations, the formation energy of defects is typically above 20kT, or fewer than 2 defects per billion structures. We also use calculations based on the string method to explore the most probable transition pathways during the melting of defects into perfect cylinders. From our string calculations, the kinetic barrier associated with the melting process is often less 1.5kT, suggesting relatively short annealing times for the complete removal of defects.