Entering edit mode

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!
Summary:
Converged in 40 iterations (1258.95 sec)
Loglikelihood: -39945324.128610
Fst divergences between estimated populations:
Pop0 Pop1 Pop2
Pop0
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 www.genetics.ucla.edu/software/admixture ****
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`

?