Problems with the aesthetics of the plot

[jacolmen]

Dear Justin,

Thanks for this amazing, super useful and straightforward tool.

I ran an analysis on two mammal genomes (both are 24 almost identical chromosomes) using the following parameters:

./jupiter name=PTru_pMa ref=../prunned_genomes/pMa.fasta fa=../prunned_genomes/pTru.fasta t=20 m=1000000 ng=99 labels=both i=24

Here I attach the png output, which I consider is a little bit weird in terms of the colors of the polygons representing the chromosomes of my reference. Do you know the reason I'm getting those colors? I know that one can set the colors manually in the karyotype file but when I see analyses from other users (as well as the example in your github) colors are different even when running default parameters. I would appreciate if you can tell me if I'm making some mistakes.

Have a good week,

Javier C.