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irycisBioinfo / PATO

PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
GNU General Public License v3.0
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mmseqs #4

Closed hooney91 closed 2 years ago

hooney91 commented 2 years ago

Hello

When I run the mmseqs command i got the error

Error in if (grepl("AVX2", system("sysctl -a | grep 'AVX2'", intern = T))) { : argument is of length zero In addition: Warning message: In system("sysctl -a | grep 'AVX2'", intern = T) : running command 'sysctl -a | grep 'AVX2'' had status 1

The script I used to run it is attached below.

load gff files

gff_list = dir(path = "./gff", pattern = ".gff", full.names = T) gff = load_gff_list(gff_list)

classifier

species = classifier(gff, n_cores = 6, type = "wgs") species %>% group_by(organism_name) %>% summarise(Number = n())

MMseq (Many-against-Many sequence searching)

mm = mmseqs(gff, type = "prot")

Thanks

valflanza commented 2 years ago

Hello.

What OS are you using? (Windows, Linux, Mac...) and if it is Linux what Distro?

hooney91 commented 2 years ago

I am using a mac with apple silicon.

valflanza commented 2 years ago

Can you try "Sys.getenv("R_PLATFORM")" and tell me what it answer?

hooney91 commented 2 years ago

The following message is output. "aarch64-apple-darwin20"

hooney91 commented 2 years ago

The error was fixed after a recent update. Thank you.