I am trying to get my PHG imputation pipeline running. I use a small reference panel and a large low-coverage nested population to be imputed. The first part of the pipeline run properly, creating the pangenome.fa, aligning the read using minimap2, but after it made the graph, an error message appears:
[pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createEdges: creating edges from nodes. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createEdges: time:1.35681E-4 secs. [pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - bound must be positive.
Then it points to the DiplodPathPlugin and finalises reporting the same "bounds must be positive" error. Also, it doesn't write any output. I checked the key file for the proper setup, and it's ok.
Could you please give me some advice to overcome this error? Thanks a lot!