ADMIXTURE, size of .bed file not matching number of individuals in analysis
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4.2 years ago
beausoleilmo ▴ 370

When I run an ADMIXTURE analysis I don't have, in the output, the number of individuals that I have in my input file (93 in the output vs 96 in the input).

# To calculate ancestry stuff:
admixture Finches_noSca.bed 4 # -j8 this last flag is to increase the number of cores! 

Converged in 40 iterations (1258.95 sec)
Loglikelihood: -39945324.128610
Fst divergences between estimated populations: 
    Pop0    Pop1    Pop2    
Pop1    0.016   
Pop2    0.043   0.041   
Pop3    0.014   0.017   0.041   
Writing output files.

# Will output this: 
Finches_noSca.4.Q Finches_noSca.4.P

Does it have something to do with this:

****                   ADMIXTURE Version 1.3.0                  ****
****                    Copyright 2008-2015                     ****
****           David Alexander, Suyash Shringarpure,            ****
****                John  Novembre, Ken Lange                   ****
****                                                            ****
****                 Please cite our paper!                     ****
****   Information at  ****

Cross-validation will be performed.  Folds=5.
Random seed: 43
Point estimation method: Block relaxation algorithm
Convergence acceleration algorithm: QuasiNewton, 3 secant conditions
Point estimation will terminate when objective function delta < 0.0001
Estimation of standard errors disabled; will compute point estimates only.
Size of G: 93x840907
Performing five EM steps to prime main algorithm

The 3 secant conditions?

ADMIXTURE • 1.6k views

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