Currently you must run prodigal and then convert its output to GFF3 format and provide it to the pred_gff option in the control files. Integrated execution of prodigal (I.e. MAKER runs it for you and then reads the native output) has been requested, but is not yet available. For now on prokaryotes, GeneMark is the only predictor natively executed with other programs having to use the pred_gff option. This will change though (I.e. the very fact you are asking for prodigal will make the pending update move closer to the top of the MAKER priority list).