Karyotype "Error: some genes in blocks can't be found, please rerun after making sure that bed file agree with simple file."

[jmpolinski]

I can trying to create a macrosynteny figure with 3 genomes, but keep getting the error that the genes in the second simple file cannot be found in the bed files. It is every line of the simple file.

I know the bed and simple files are ok because karyotype works fine when only run on sets of 2 with the same bed and simple files. I've checked the layout and seqids files multiple times (work fine when one or the 3 is commented out -- attached).

layout.txt
seqids.txt
output.txt

[sunshichao0916]

Hi jmpolinski, I met the same problem. How did you solve it? Can you give me some suggestions?

[crz-ops]

Hi jmpolinski, I met the same problem. How did you solve it? Can you give me some suggestions?

The problem lies in the layout file. We need to draw edges between the tracks, and same edges should not appear multiple times.
for example, "e,0,1" asks to draw edges between track 0 and 1, so the next part should be e,1,2 instead of e,0,1.

[wcwongay]

Hi jmpolinski, I met the same problem. How did you solve it? Can you give me some suggestions?

The problem lies in the layout file. We need to draw edges between the tracks, and same edges should not appear multiple times. for example, "e,0,1" asks to draw edges between track 0 and 1, so the next part should be e,1,2 instead of e,0,1.

I changed the layout file as well, but I still encountered this problem when I was trying to plot three species together.

[oddguyeee]

Please check the layout.txt carefully, especially in edges section.