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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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core_genome #5

Closed hooney91 closed 2 years ago

hooney91 commented 2 years ago

When I run the core_gene 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.

nr_files = nr_list %>% as.data.frame() %>% group_by(cluster) %>% top_n(1, centrality) %>% summarise_all(first) %>% select(Source) %>% distinct()

core = mmseqs(nr_files) %>% core_genome(type = "prot", n_cores = 6)

Additionally, I am using a mac with apple silicon (aarch64-apple-darwin20).

valflanza commented 2 years ago

It is a problem related to the new Apple processors for Mac. We have already solved it. Please update the package.