search

sgearle / bugwas

Locus and lineage tests for bacterial GWAS
GNU General Public License v2.0
30 stars 5 forks source link

bugwas question #8

Closed ycgong closed 7 years ago

ycgong commented 7 years ago

Running the example data with lin_loc it returns an error line and doesn't finish:

data <- lin_loc(gen = gen, pheno = pheno, phylo = phylo,prefix = prefix, gem.path = "./gemma") Error in checkExistence(arg) : The file does not exist!

Tried to use a new version of gemma (0.94.1) and even link gemma to /usr/local/bin, but that didn't solve the problem.

sgearle commented 7 years ago

The gemma version used must be our modified version 0.93 which can be downloaded from the bugwas github repository in the gemma folder. The error received means that one of your input files doesn't exist.

ycgong commented 7 years ago

Thanks @sgearle it works.