Question: ADMIXTURE, size of .bed file not matching number of individuals in analysis
gravatar for beausoleilmo
3.0 years ago by
McGill University
beausoleilmo270 wrote:

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 • 1.2k views
ADD COMMENTlink written 3.0 years ago by beausoleilmo270
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2304 users visited in the last hour