A value this high likely means your data is too diverse to construct a useful pangenome graph from.

[ld9866]

Dear developer:

I built a pan-genome of our different individuals using Minigraph-cactus, and he did a very good job of finding a lot of key variation information.

But I was mistaken for ascension after adding individuals of several near-origin species. I would like to ask how we can solve this problem?

Best day! Dong

Code： docker run -it -v /home/test/nvmedata2/MC:/data quay.io/comparative-genomics-toolkit/cactus:v2.9.0-gpu cactus-pangenome ./js ./test.list --outDir test.result --outName test.result --reference reference --vcf --giraffe --gfa --gbz --maxCores 96 --maxMemory 850G

WARNING: Sample Pop1 has mash distance 0.0210181 from the reference. A value this high likely means your data is too diverse to construct a useful pangenome graph from.

[glennhickey]

It gives that warning for anything over 0.02. You're not that far over, so it could be your data is fine. You can check the coverage with halCoverage or halStats or vg paths -Ev to make sure.

[ld9866]

Thank you! We deleted some distant individuals and everything worked out fine