Convertf error "fatalx: no valid samples!"
inezd24 opened this issue · comments
Hi,
I've used convertf many times without issues, but am now running into a problem where it doesn't consider my samples valid. I am trying to convert bed/bim/fam files to geno/snp/ind files retaining a subset of individuals with the following par.file:
echo par.file.eig
genotypename: subset.bed
snpname: subset.bim
indivname: subset.fam
outputformat: EIGENSTRAT
genotypeoutname: subset_fst.geno
snpoutname: subset_fst.snp
indivoutname: subset_fst.ind
poplistname: subset_individuals.txt
I've also attempted running it with different outputformats, e.g. PACKEDANCESTRYMAP or without a specified outputformat line.
Using the following command:
~/eigensoft/EIG-7.2.1/bin/convertf -p ./par.file.eig > ./out_convert.log
Generates the following log:
fatalx:
no valid samples!
Aborted (core dumped)
What might explain the software to consider my samples invalid? Here's a head of my .fam file:
Akha Akha25 0 0 2 1
Akha Akha26 0 0 1 1
Ami Ami1 0 0 1 1
Ami Ami2 0 0 1 1
and here's a head of my .bim file:
1 1_1158277 0.013 1158277 A G
1 1_1776269 0 1776269 A C
1 1_1852484 0 1852484 G A
1 1_1930754 0.021 1930754 T C
