MCScanX Error - Can't plot the graphs (Downstream analysis)

Question

[oliveira.bhn]

Hi, everyone!

I am trying to use the MCScanX tool for ploting circular displays of syntenic genomic blocks.

When I try running $ java circle_plotter -g gff_file -s collinearity_file -c control_file -o output_PNG_file

I get the follwing error: Exception in thread "main" java.lang.NullPointerException at circle_plotter.paint(circle_plotter.java:142) at circle_plotter.main(circle_plotter.java:262)

Does anyone know how to solve it?

Many thanks in advance.

Answer 1

[Lhl]

I ran into the same error, I wonder if you have solved the issue.

Answer 2

[xhyan1012]

This error may happen because you haven't revised the circle.ctl file. You should specify what genomic blocks should be plotted and add your genomic blocks to the control file manually. More details can be found in issue on github.