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Convertf error "fatalx: no valid samples!" #102

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inezd24 opened this issue Jan 4, 2024 · 1 comment
Open

Convertf error "fatalx: no valid samples!" #102

inezd24 opened this issue Jan 4, 2024 · 1 comment

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@inezd24
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inezd24 commented Jan 4, 2024

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
@liamxg
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liamxg commented Jun 4, 2024

Dear @inezd24,

you .bim file look like snp file?

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