Even if you have metallic electrodes, you can still have a transport gap, because the transmission spectrum is also determined by the central /scattering region that have a carbon chain with the electronic properties different from that of the electrodes. You may have resonances, Fano resonances and so on, depending on how the energy levels of the chain are aligned with the Fermi level given by the metal electrodes, as well as on the level broadening given by the coupling to the electrodes.
I would suggest doing a literature search and reading some papers to better analyze your results.
You may also calculate the energy levels of isolated chain and/or the transmission as a function of separation distance between the chain and electrode. You should also compute more analysis objects, e.g., PLDOS across the device.
