wide self and close groups assigned/ WARNING: Cannot cluster close group using KDE/ no close.kde.png out

[meisiy]

I ran hgtector analyze step for 67 genomes classified as under the genus Pseuomdonas_E by GTDB.

In the log file, I found that:

1. One genome (P36) has been assign to Gammaproteobacteria, others are Pseudomonas;
2. The self group and close group are assigned to the wider classifications (class, phylum) , did P36 cause this situation? Will such a wider classification result in accurate output?

All input genomes belong to 1236 (class Gammaproteobacteria). Auto-inferred self group: 1236 (class Gammaproteobacteria) Self group has 9266 taxa. Auto-inferred close group: 1224 (phylum Proteobacteria) Close group has 10062 taxa.

And there is 2 warnings:
WARNING: Cannot cluster close group using KDE. Use fixed threshold 25 instead. Threshold: 2.41772. Distal group: 1.000: n/a 0.886: n/a 0.785: n/a 0.695: n/a 0.616: n/a 0.546: n/a 0.483: n/a 0.428: n/a 0.379: n/a 0.336: n/a 0.298: n/a 0.264: n/a 0.234: n/a 0.207: 16.7715 - 88.75% 0.183: 16.4382 - 88.61% 0.162: 16.2809 - 88.52% 0.144: 16.1873 - 88.49% 0.127: 16.1199 - 88.46% 0.113: 16.0749 - 88.45% 0.100: 12.9251 - 86.93% WARNING: Cannot cluster distal group using KDE. Use fixed threshold 25 instead. Threshold: 0. Done.

In the result file, I see no close.kde.png:

close hist
distal hist
scatter
Are these figures normal?