smartPCA: problem with .evec file

smartPCA: problem with .evec file

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Hi all!
I’m having problems with .evec file when running smartPCA. This file doesn’t consider all the individuals that I introduced in .ped file (529 individuals).

Anyone knows what the problem might be?
The command that I used was:
./smartpca -p Patag_sud_maf_ld.par > Patag_sud_maf_ld.out

The .par file contains:

genotypename: Patag_sud_maf_ld.ped
snpname: Patag_sud_maf_ld.map
indivname: Patag_sud_maf_ld.ped
evecoutname: Patag_sud_maf_ld.evec
evaloutname: Patag_sud_maf_ld.eval
numoutlieriter: 0

I will apreciate your answer!


file


evec


smartpca

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