Truncated proteins at genome end

[ilyavs]

Hi, I am encountering cases where there are truncated proteins (missing stop codon) called by phanotate at the genome end. The common case was when there was another protein on the other side of the contig which was missing a start codon. Thus, when rotating the genome, a complete CDS would be found. However, after rotating the genome, I still see rare cases of truncated proteins at genome end for which I can't find a logical continuation on the other side of the contig. Is this the intended behavior? Should I discard these proteins in post processing? Thanks, Ilya.