Problem of the result of LoReAn

[LiantingFu]

Hello! I used LoReAn for genome annotation, but I have encountered some problems. I found that most of gene and mRNA sequences in LoReAn result are incomplete. Here is an example. As the screenshot of IGV shows, the first track is the result of Liftoff, which is got by lifting genome annotations from a closely-related species, and the second track is the result of LoReAn. I wonder if I made some mistakes when I was using LoReAn. Could you please give me some advice? Thank you very much!