ADMIXTOOLS: qp3pop fatal error (probably missing pop)

Hello! I want to run qp3Pop from ADMIXTOOLS and determine which population is more similar to my sample. I have merged data from 26 populations from 1000 genomes with my data and tried to run

$HOME/bin/qp3Pop -p par.qp3pop >logfile

Where the par.qp3pop file is

genotypename: dataset.geno
snpname: dataset.snp
indivname: dataset.ind
popfilename: poplist_qp3test
inbreed: YES

And the error message is

fatal error  (probably missing pop) 
Aborted (core dumped)

What is the issue here? The logfile is not esplicative. This is my poplist_qp3test file

Population1.SG Mysample Mbuti.DG
Population2.SG Mysample Mbuti.DG
Population26.SG Mysample Mbuti.DG

And this is the logfile

THE INPUT PARAMETERS
PARAMETER NAME: VALUE
genotypename: dataset.geno
snpname: dataset.snp
indivname: dataset.ind
popfilename: poplist_qp3test
inbreed: YES
qp3Pop version: 651
inbreed set YES
number of triples 27
nplist: 27
snps: 1150548
number of blocks for block jackknife: 714
pop:  ACB.SG
pop:  Mysample
pop:  Mbuti.DG

What am I doing wrong?

Thanks!

qp3pop f3test admixtools

• 1,488 views • link

updated 1.3 years ago by Duy •

• written 4.1 years ago by francesco.fontani2 •

1 answer

To all the future viewers who might experience this problem, I updated the third column in my .ind file to the corresponding population name for each samples and it worked!

If you are running the analysis on a Linux or Mac system, you can use the admixr package in R to simplify your workflow (I ran it on Windows with Linux as my subsystem so I could not link AdmixTools path to R environment, as AdmixTools only runs in Linux/Mac).

Here is the command line that I used to update the third column: gawk -i inplace '{split($1,id,":"); $3=id[1]; print $0}' yourfile.ind .

• 0 views • link

written 1.3 years ago by Duy •