The file format input must be Genbank (.gbk or .gb) format post annotation (automatic or manual). We have gone over programs to accomplish this if you have genomes. If you are downloading them from NCBI's Genbank - you have to be particular to have all the information. Make sure you add the sequence to the genbank file (outlined in the screen shot below). And make sure it downloads fully before going to Send -> File -> Create File (otherwise you download a fraction of the GenBank).
