core_genome() function

[jhcuarta]

Hi

When I run the core_genome command i got the following error

core <- core_genome(mm, type = 'prot', n_cores = 6, method = "accurate")
Joining, by = "head"
Error in core_genome(mm, type = "prot", n_cores = 6, method = "accurate") :
No core_genome found

This is the script I've been running

library(V8)
library(pato)
library(dplyr)
library(tidyr)
library(tibble)
library(dtplyr)
library(foreach)
library(doParallel)
library(parallel)
gff_files <- dir("/home/jason/Documentos/PATO_vibrio/gff_143", pattern = ".gff", full.names = T)
gffs <- load_gff_list(gff_files)
my_mash <- mash(gffs, type ="prot")
species <- classifier(gffs, n_cores = 6, type = 'prot')
species %>% group_by(organism_name) %>% summarise(Number = n())
my_mmseq <- mmseqs(gff_files, coverage = 0.8, identity = 0.8, evalue = 1e-6, n_cores = 6, cov_mode = 0, cluster_mode = 0)
my_accnet <- accnet(my_mmseq, threshold = 0.8, singles = FALSE)
mm <- mmseqs(gffs, type = "prot")
core <- core_genome(mm, type = 'prot', n_cores = 6, method = "accurate")

Regards

[valflanza]

It seems that in your samples it does not find any genes that form a core genome. In other words, there is no common gene in your samples.

What bacteria are you analyzing and how many are they?

[jhcuarta]

Hi
143 Vibrio cholerae genomes, 92 complete, and 51 draft. It seems odd since I've run other pangenome tools