search

irycisBioinfo / PATO

PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
GNU General Public License v3.0
58 stars 6 forks source link

core_genome() function #2

Open jhcuarta opened 3 years ago

jhcuarta commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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