I generated the BLAST hits file using diamond not by blast, is that the problem?

[zx0223winner]

Hi I see where is the problem, don’t worry about the diamond Blast and the length file are all correct. However, you did the blast all-against-all not on your genome itself. You have to make sure you use the same gene ID not different types (e.g., g1478.t1 is where you de novo assembled, XP_027134523.1 is from NCBI). Keep one type of gene ID for all.

So I suggest you Blast Aven.fa proteins against itself.
~Xi