load_gff_list() error

[kazumaxneo]

Hi,

I am interested in PATO's dn_ds() functin and installed PATO in my R 4.1.1 enviroment (os: ubuntu18).
But, I got the following error when using load_gff_list() to to load my GFF lists.

library(pato)
gff_files <- dir("./GFF_dir", pattern = ".gff", full.names = T)
gffs <- load_gff_list(gff_files)

#error message
Error in socketAccept(socket = socket, blocking = TRUE, open = "a+b", :
all connections are in use

My GFF files were created using prokka.
I do not think there is a problem with the format of the my GFF files since it can be used by other pan-genomic analysis tools (e.g. roary).

[valflanza]

Seems to be a problem with parallel processing. Try running using a single core with the "n_cores = 1" parameter.

Please remember that dn_ds function is still in beta version but we are glad to get feedback.

[kazumaxneo]

Hi valflanza.

Wow, this option worked well in my environment.

Thanks also for the dn_ds() functin (status: beta).

Thank you very much.