Gila trout workaround

What you need to do

1. Download gila-trout.zip

2. Unizip it in the directory where you want to work. Make sure that it creates a directory called gila-trout.stru.snmf. If it does, check to make sure that it has directories K2 through K110. If it does, you should be all set.

3. Download trout.Rsave and save it in the directory where you plan to work. gila-trout.stru.snmf should be in this directory.

Now you should be able to plot the cross-entropy graph using plot() as described in the documentation for LEA, and you should be able to use plot_LEA() to produce the barplot.

What I did to produce the files

Here’s how I run the data

library(LEA)

package ‘LEA’ was built under R version 4.0.3

trout <- snmf("gila-trout.stru.geno", K = 2:10, repetitions = 10, 
              project = "new", 
              entropy = TRUE)

The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] 998871170
[1] "*************************************"
[1] "*          create.dataset            *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)                 154
        -L (number of loci)                        2381
        -s (seed random init)                      998871170
        -r (percentage of masked data)             0.05
        -x (genotype file in .geno format)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -o (output file in .geno format)           /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno

 Write genotype file with masked data, /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.

[1] "*************************************"
[1] "* sNMF K = 2  repetition 1      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          2
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run1/gila-trout.stru_r1.2.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run1/gila-trout.stru_r1.2.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  18178740354
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==================]
Number of iterations: 49

Least-square error: 134090.250512
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run1/gila-trout.stru_r1.2.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run1/gila-trout.stru_r1.2.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      2
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run1/gila-trout.stru_r1.2.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run1/gila-trout.stru_r1.2.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.608429
Cross-Entropy (masked data):     0.62593
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 3  repetition 1      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          3
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run1/gila-trout.stru_r1.3.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run1/gila-trout.stru_r1.3.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  9588805762
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [====================]
Number of iterations: 54

Least-square error: 121441.934242
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run1/gila-trout.stru_r1.3.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run1/gila-trout.stru_r1.3.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      3
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run1/gila-trout.stru_r1.3.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run1/gila-trout.stru_r1.3.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.535696
Cross-Entropy (masked data):     0.564744
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 4  repetition 1      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          4
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run1/gila-trout.stru_r1.4.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run1/gila-trout.stru_r1.4.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201616314498
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [========]
Number of iterations: 21

Least-square error: 112109.961153
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run1/gila-trout.stru_r1.4.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run1/gila-trout.stru_r1.4.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      4
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run1/gila-trout.stru_r1.4.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run1/gila-trout.stru_r1.4.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.484225
Cross-Entropy (masked data):     0.521256
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 5  repetition 1      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          5
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run1/gila-trout.stru_r1.5.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run1/gila-trout.stru_r1.5.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201616314498
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [============================]
Number of iterations: 75

Least-square error: 108505.120635
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run1/gila-trout.stru_r1.5.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run1/gila-trout.stru_r1.5.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      5
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run1/gila-trout.stru_r1.5.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run1/gila-trout.stru_r1.5.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.466086
Cross-Entropy (masked data):     0.513375
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 6  repetition 1      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          6
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run1/gila-trout.stru_r1.6.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run1/gila-trout.stru_r1.6.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201616314498
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [========================]
Number of iterations: 64

Least-square error: 105447.507053
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run1/gila-trout.stru_r1.6.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run1/gila-trout.stru_r1.6.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      6
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run1/gila-trout.stru_r1.6.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run1/gila-trout.stru_r1.6.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.450395
Cross-Entropy (masked data):     0.508397
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 7  repetition 1      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          7
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run1/gila-trout.stru_r1.7.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run1/gila-trout.stru_r1.7.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201616314498
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [================]
Number of iterations: 44

Least-square error: 103974.612133
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run1/gila-trout.stru_r1.7.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run1/gila-trout.stru_r1.7.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      7
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run1/gila-trout.stru_r1.7.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run1/gila-trout.stru_r1.7.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.446261
Cross-Entropy (masked data):     0.509675
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 8  repetition 1      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          8
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run1/gila-trout.stru_r1.8.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run1/gila-trout.stru_r1.8.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4607182419798888578
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========================================]
Number of iterations: 112

Least-square error: 101977.488273
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run1/gila-trout.stru_r1.8.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run1/gila-trout.stru_r1.8.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      8
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run1/gila-trout.stru_r1.8.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run1/gila-trout.stru_r1.8.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.436581
Cross-Entropy (masked data):     0.510568
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 9  repetition 1      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          9
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run1/gila-trout.stru_r1.9.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run1/gila-trout.stru_r1.9.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201616314498
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 27

Least-square error: 100920.195670
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run1/gila-trout.stru_r1.9.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run1/gila-trout.stru_r1.9.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      9
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run1/gila-trout.stru_r1.9.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run1/gila-trout.stru_r1.9.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.433581
Cross-Entropy (masked data):     0.514196
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 10  repetition 1      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          10
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run1/gila-trout.stru_r1.10.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run1/gila-trout.stru_r1.10.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4621819118587842690
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=======================]
Number of iterations: 62

Least-square error: 98919.796490
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run1/gila-trout.stru_r1.10.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run1/gila-trout.stru_r1.10.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      10
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run1/gila-trout.stru_r1.10.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run1/gila-trout.stru_r1.10.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.423017
Cross-Entropy (masked data):     0.511088
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] 781499922
[1] "*************************************"
[1] "*          create.dataset            *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)                 154
        -L (number of loci)                        2381
        -s (seed random init)                      781499922
        -r (percentage of masked data)             0.05
        -x (genotype file in .geno format)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -o (output file in .geno format)           /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno

 Write genotype file with masked data, /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.

[1] "*************************************"
[1] "* sNMF K = 2  repetition 2      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          2
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run2/gila-trout.stru_r2.2.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run2/gila-trout.stru_r2.2.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201398943250
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==================]
Number of iterations: 47

Least-square error: 134053.756217
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run2/gila-trout.stru_r2.2.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run2/gila-trout.stru_r2.2.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      2
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run2/gila-trout.stru_r2.2.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run2/gila-trout.stru_r2.2.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.607766
Cross-Entropy (masked data):     0.636004
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 3  repetition 2      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          3
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run2/gila-trout.stru_r2.3.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run2/gila-trout.stru_r2.3.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  9371434514
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=========]
Number of iterations: 24

Least-square error: 121263.358361
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run2/gila-trout.stru_r2.3.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run2/gila-trout.stru_r2.3.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      3
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run2/gila-trout.stru_r2.3.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run2/gila-trout.stru_r2.3.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.535181
Cross-Entropy (masked data):     0.573382
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 4  repetition 2      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          4
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run2/gila-trout.stru_r2.4.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run2/gila-trout.stru_r2.4.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  430278229522
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 26

Least-square error: 112095.088270
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run2/gila-trout.stru_r2.4.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run2/gila-trout.stru_r2.4.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      4
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run2/gila-trout.stru_r2.4.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run2/gila-trout.stru_r2.4.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.483778
Cross-Entropy (masked data):     0.525346
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 5  repetition 2      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          5
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run2/gila-trout.stru_r2.5.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run2/gila-trout.stru_r2.5.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201398943250
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [======================]
Number of iterations: 58

Least-square error: 108536.235400
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run2/gila-trout.stru_r2.5.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run2/gila-trout.stru_r2.5.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      5
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run2/gila-trout.stru_r2.5.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run2/gila-trout.stru_r2.5.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.465332
Cross-Entropy (masked data):     0.516879
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 6  repetition 2      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          6
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run2/gila-trout.stru_r2.6.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run2/gila-trout.stru_r2.6.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201398943250
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [========================]
Number of iterations: 65

Least-square error: 105601.331757
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run2/gila-trout.stru_r2.6.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run2/gila-trout.stru_r2.6.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      6
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run2/gila-trout.stru_r2.6.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run2/gila-trout.stru_r2.6.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.450635
Cross-Entropy (masked data):     0.509827
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 7  repetition 2      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          7
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run2/gila-trout.stru_r2.7.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run2/gila-trout.stru_r2.7.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201398943250
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=============]
Number of iterations: 34

Least-square error: 103942.189349
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run2/gila-trout.stru_r2.7.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run2/gila-trout.stru_r2.7.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      7
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run2/gila-trout.stru_r2.7.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run2/gila-trout.stru_r2.7.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.445392
Cross-Entropy (masked data):     0.511922
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 8  repetition 2      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          8
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run2/gila-trout.stru_r2.8.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run2/gila-trout.stru_r2.8.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  9371434514
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===================]
Number of iterations: 52

Least-square error: 102012.787046
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run2/gila-trout.stru_r2.8.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run2/gila-trout.stru_r2.8.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      8
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run2/gila-trout.stru_r2.8.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run2/gila-trout.stru_r2.8.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.437278
Cross-Entropy (masked data):     0.51448
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 9  repetition 2      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          9
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run2/gila-trout.stru_r2.9.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run2/gila-trout.stru_r2.9.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201398943250
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [======================]
Number of iterations: 59

Least-square error: 101042.015596
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run2/gila-trout.stru_r2.9.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run2/gila-trout.stru_r2.9.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      9
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run2/gila-trout.stru_r2.9.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run2/gila-trout.stru_r2.9.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.431659
Cross-Entropy (masked data):     0.515098
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 10  repetition 2      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          10
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run2/gila-trout.stru_r2.10.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run2/gila-trout.stru_r2.10.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201398943250
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=======]
Number of iterations: 20

Least-square error: 99042.357124
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run2/gila-trout.stru_r2.10.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run2/gila-trout.stru_r2.10.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      10
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run2/gila-trout.stru_r2.10.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run2/gila-trout.stru_r2.10.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.422997
Cross-Entropy (masked data):     0.51358
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] 104564860
[1] "*************************************"
[1] "*          create.dataset            *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)                 154
        -L (number of loci)                        2381
        -s (seed random init)                      104564860
        -r (percentage of masked data)             0.05
        -x (genotype file in .geno format)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -o (output file in .geno format)           /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno

 Write genotype file with masked data, /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.

[1] "*************************************"
[1] "* sNMF K = 2  repetition 3      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          2
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run3/gila-trout.stru_r3.2.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run3/gila-trout.stru_r3.2.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  12989466748
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [================]
Number of iterations: 43

Least-square error: 134194.836260
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run3/gila-trout.stru_r3.2.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run3/gila-trout.stru_r3.2.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      2
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run3/gila-trout.stru_r3.2.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run3/gila-trout.stru_r3.2.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.608393
Cross-Entropy (masked data):     0.625736
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 3  repetition 3      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          3
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run3/gila-trout.stru_r3.3.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run3/gila-trout.stru_r3.3.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140200722008188
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===========]
Number of iterations: 29

Least-square error: 121376.845371
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run3/gila-trout.stru_r3.3.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run3/gila-trout.stru_r3.3.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      3
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run3/gila-trout.stru_r3.3.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run3/gila-trout.stru_r3.3.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.536052
Cross-Entropy (masked data):     0.559264
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 4  repetition 3      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          4
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run3/gila-trout.stru_r3.4.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run3/gila-trout.stru_r3.4.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140200722008188
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 27

Least-square error: 112127.640545
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run3/gila-trout.stru_r3.4.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run3/gila-trout.stru_r3.4.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      4
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run3/gila-trout.stru_r3.4.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run3/gila-trout.stru_r3.4.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.484198
Cross-Entropy (masked data):     0.518333
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 5  repetition 3      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          5
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run3/gila-trout.stru_r3.5.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run3/gila-trout.stru_r3.5.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140200722008188
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [====================]
Number of iterations: 53

Least-square error: 108703.410061
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run3/gila-trout.stru_r3.5.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run3/gila-trout.stru_r3.5.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      5
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run3/gila-trout.stru_r3.5.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run3/gila-trout.stru_r3.5.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.465591
Cross-Entropy (masked data):     0.509282
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 6  repetition 3      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          6
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run3/gila-trout.stru_r3.6.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run3/gila-trout.stru_r3.6.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  104564860
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========================]
Number of iterations: 69

Least-square error: 105543.926157
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run3/gila-trout.stru_r3.6.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run3/gila-trout.stru_r3.6.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      6
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run3/gila-trout.stru_r3.6.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run3/gila-trout.stru_r3.6.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.450804
Cross-Entropy (masked data):     0.503107
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 7  repetition 3      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          7
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run3/gila-trout.stru_r3.7.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run3/gila-trout.stru_r3.7.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140200722008188
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==============]
Number of iterations: 37

Least-square error: 103793.648116
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run3/gila-trout.stru_r3.7.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run3/gila-trout.stru_r3.7.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      7
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run3/gila-trout.stru_r3.7.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run3/gila-trout.stru_r3.7.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.445067
Cross-Entropy (masked data):     0.502736
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 8  repetition 3      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          8
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run3/gila-trout.stru_r3.8.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run3/gila-trout.stru_r3.8.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140200722008188
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===============]
Number of iterations: 40

Least-square error: 102014.883563
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run3/gila-trout.stru_r3.8.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run3/gila-trout.stru_r3.8.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      8
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run3/gila-trout.stru_r3.8.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run3/gila-trout.stru_r3.8.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.436744
Cross-Entropy (masked data):     0.501553
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 9  repetition 3      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          9
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run3/gila-trout.stru_r3.9.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run3/gila-trout.stru_r3.9.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140200722008188
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=====================]
Number of iterations: 56

Least-square error: 100974.657594
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run3/gila-trout.stru_r3.9.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run3/gila-trout.stru_r3.9.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      9
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run3/gila-trout.stru_r3.9.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run3/gila-trout.stru_r3.9.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.432779
Cross-Entropy (masked data):     0.506541
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 10  repetition 3      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          10
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run3/gila-trout.stru_r3.10.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run3/gila-trout.stru_r3.10.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140200722008188
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=============]
Number of iterations: 35

Least-square error: 99124.612521
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run3/gila-trout.stru_r3.10.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run3/gila-trout.stru_r3.10.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      10
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run3/gila-trout.stru_r3.10.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run3/gila-trout.stru_r3.10.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.423206
Cross-Entropy (masked data):     0.508905
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] 1129834191
[1] "*************************************"
[1] "*          create.dataset            *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)                 154
        -L (number of loci)                        2381
        -s (seed random init)                      1129834191
        -r (percentage of masked data)             0.05
        -x (genotype file in .geno format)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -o (output file in .geno format)           /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno

 Write genotype file with masked data, /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.

[1] "*************************************"
[1] "* sNMF K = 2  repetition 4      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          2
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run4/gila-trout.stru_r4.2.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run4/gila-trout.stru_r4.2.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4607182419929851599
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=================]
Number of iterations: 45

Least-square error: 134226.201492
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run4/gila-trout.stru_r4.2.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run4/gila-trout.stru_r4.2.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      2
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run4/gila-trout.stru_r4.2.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run4/gila-trout.stru_r4.2.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.608816
Cross-Entropy (masked data):     0.620183
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 3  repetition 4      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          3
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run4/gila-trout.stru_r4.3.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run4/gila-trout.stru_r4.3.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201747277519
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===========]
Number of iterations: 29

Least-square error: 121387.917879
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run4/gila-trout.stru_r4.3.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run4/gila-trout.stru_r4.3.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      3
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run4/gila-trout.stru_r4.3.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run4/gila-trout.stru_r4.3.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.535701
Cross-Entropy (masked data):     0.560273
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 4  repetition 4      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          4
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run4/gila-trout.stru_r4.4.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run4/gila-trout.stru_r4.4.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201747277519
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 26

Least-square error: 112257.133509
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run4/gila-trout.stru_r4.4.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run4/gila-trout.stru_r4.4.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      4
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run4/gila-trout.stru_r4.4.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run4/gila-trout.stru_r4.4.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.48439
Cross-Entropy (masked data):     0.518369
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 5  repetition 4      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          5
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run4/gila-trout.stru_r4.5.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run4/gila-trout.stru_r4.5.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  220173166287
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [========================]
Number of iterations: 64

Least-square error: 108491.127553
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run4/gila-trout.stru_r4.5.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run4/gila-trout.stru_r4.5.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      5
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run4/gila-trout.stru_r4.5.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run4/gila-trout.stru_r4.5.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.465226
Cross-Entropy (masked data):     0.510466
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 6  repetition 4      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          6
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run4/gila-trout.stru_r4.6.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run4/gila-trout.stru_r4.6.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201747277519
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=============================]
Number of iterations: 77

Least-square error: 105658.227308
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run4/gila-trout.stru_r4.6.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run4/gila-trout.stru_r4.6.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      6
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run4/gila-trout.stru_r4.6.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run4/gila-trout.stru_r4.6.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.451295
Cross-Entropy (masked data):     0.503375
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 7  repetition 4      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          7
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run4/gila-trout.stru_r4.7.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run4/gila-trout.stru_r4.7.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201747277519
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=====================]
Number of iterations: 56

Least-square error: 104062.660684
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run4/gila-trout.stru_r4.7.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run4/gila-trout.stru_r4.7.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      7
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run4/gila-trout.stru_r4.7.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run4/gila-trout.stru_r4.7.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.446429
Cross-Entropy (masked data):     0.505973
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 8  repetition 4      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          8
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run4/gila-trout.stru_r4.8.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run4/gila-trout.stru_r4.8.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4607182419929851599
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [================]
Number of iterations: 42

Least-square error: 102148.694628
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run4/gila-trout.stru_r4.8.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run4/gila-trout.stru_r4.8.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      8
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run4/gila-trout.stru_r4.8.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run4/gila-trout.stru_r4.8.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.437074
Cross-Entropy (masked data):     0.505782
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 9  repetition 4      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          9
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run4/gila-trout.stru_r4.9.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run4/gila-trout.stru_r4.9.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201747277519
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===============]
Number of iterations: 40

Least-square error: 100330.492960
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run4/gila-trout.stru_r4.9.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run4/gila-trout.stru_r4.9.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      9
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run4/gila-trout.stru_r4.9.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run4/gila-trout.stru_r4.9.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.428601
Cross-Entropy (masked data):     0.503101
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 10  repetition 4      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          10
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run4/gila-trout.stru_r4.10.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run4/gila-trout.stru_r4.10.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201747277519
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [================]
Number of iterations: 44

Least-square error: 99074.110270
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run4/gila-trout.stru_r4.10.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run4/gila-trout.stru_r4.10.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      10
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run4/gila-trout.stru_r4.10.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run4/gila-trout.stru_r4.10.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.422985
Cross-Entropy (masked data):     0.505307
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] 686561465
[1] "*************************************"
[1] "*          create.dataset            *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)                 154
        -L (number of loci)                        2381
        -s (seed random init)                      686561465
        -r (percentage of masked data)             0.05
        -x (genotype file in .geno format)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -o (output file in .geno format)           /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno

 Write genotype file with masked data, /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.

[1] "*************************************"
[1] "* sNMF K = 2  repetition 5      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          2
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run5/gila-trout.stru_r5.2.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run5/gila-trout.stru_r5.2.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  686561465
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===========]
Number of iterations: 30

Least-square error: 133972.697967
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run5/gila-trout.stru_r5.2.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run5/gila-trout.stru_r5.2.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      2
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run5/gila-trout.stru_r5.2.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run5/gila-trout.stru_r5.2.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.608348
Cross-Entropy (masked data):     0.63088
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 3  repetition 5      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          3
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run5/gila-trout.stru_r5.3.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run5/gila-trout.stru_r5.3.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201304004793
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 28

Least-square error: 121404.332780
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run5/gila-trout.stru_r5.3.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run5/gila-trout.stru_r5.3.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      3
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run5/gila-trout.stru_r5.3.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run5/gila-trout.stru_r5.3.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.535787
Cross-Entropy (masked data):     0.566841
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 4  repetition 5      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          4
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run5/gila-trout.stru_r5.4.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run5/gila-trout.stru_r5.4.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  686561465
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 26

Least-square error: 112228.705515
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run5/gila-trout.stru_r5.4.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run5/gila-trout.stru_r5.4.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      4
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run5/gila-trout.stru_r5.4.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run5/gila-trout.stru_r5.4.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.48405
Cross-Entropy (masked data):     0.525436
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 5  repetition 5      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          5
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run5/gila-trout.stru_r5.5.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run5/gila-trout.stru_r5.5.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201304004793
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [========================]
Number of iterations: 63

Least-square error: 108372.368582
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run5/gila-trout.stru_r5.5.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run5/gila-trout.stru_r5.5.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      5
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run5/gila-trout.stru_r5.5.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run5/gila-trout.stru_r5.5.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.46515
Cross-Entropy (masked data):     0.518005
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 6  repetition 5      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          6
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run5/gila-trout.stru_r5.6.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run5/gila-trout.stru_r5.6.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4621819118275532985
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [========================]
Number of iterations: 65

Least-square error: 105562.258633
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run5/gila-trout.stru_r5.6.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run5/gila-trout.stru_r5.6.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      6
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run5/gila-trout.stru_r5.6.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run5/gila-trout.stru_r5.6.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.450648
Cross-Entropy (masked data):     0.512086
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 7  repetition 5      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          7
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run5/gila-trout.stru_r5.7.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run5/gila-trout.stru_r5.7.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  686561465
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [============]
Number of iterations: 32

Least-square error: 103516.124561
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run5/gila-trout.stru_r5.7.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run5/gila-trout.stru_r5.7.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      7
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run5/gila-trout.stru_r5.7.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run5/gila-trout.stru_r5.7.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.44427
Cross-Entropy (masked data):     0.51376
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 8  repetition 5      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          8
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run5/gila-trout.stru_r5.8.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run5/gila-trout.stru_r5.8.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  686561465
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [================]
Number of iterations: 44

Least-square error: 101934.227732
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run5/gila-trout.stru_r5.8.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run5/gila-trout.stru_r5.8.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      8
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run5/gila-trout.stru_r5.8.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run5/gila-trout.stru_r5.8.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.436983
Cross-Entropy (masked data):     0.512317
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 9  repetition 5      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          9
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run5/gila-trout.stru_r5.9.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run5/gila-trout.stru_r5.9.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201304004793
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===================]
Number of iterations: 50

Least-square error: 101023.944347
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run5/gila-trout.stru_r5.9.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run5/gila-trout.stru_r5.9.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      9
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run5/gila-trout.stru_r5.9.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run5/gila-trout.stru_r5.9.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.430608
Cross-Entropy (masked data):     0.509317
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 10  repetition 5      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          10
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run5/gila-trout.stru_r5.10.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run5/gila-trout.stru_r5.10.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201304004793
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [============]
Number of iterations: 32

Least-square error: 99128.028889
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run5/gila-trout.stru_r5.10.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run5/gila-trout.stru_r5.10.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      10
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run5/gila-trout.stru_r5.10.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run5/gila-trout.stru_r5.10.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.423641
Cross-Entropy (masked data):     0.514368
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] 1692712195
[1] "*************************************"
[1] "*          create.dataset            *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)                 154
        -L (number of loci)                        2381
        -s (seed random init)                      1692712195
        -r (percentage of masked data)             0.05
        -x (genotype file in .geno format)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -o (output file in .geno format)           /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno

 Write genotype file with masked data, /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.

[1] "*************************************"
[1] "* sNMF K = 2  repetition 6      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          2
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run6/gila-trout.stru_r6.2.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run6/gila-trout.stru_r6.2.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140202310155523
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=======]
Number of iterations: 19

Least-square error: 134061.365588
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run6/gila-trout.stru_r6.2.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run6/gila-trout.stru_r6.2.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      2
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run6/gila-trout.stru_r6.2.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run6/gila-trout.stru_r6.2.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.608504
Cross-Entropy (masked data):     0.623875
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 3  repetition 6      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          3
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run6/gila-trout.stru_r6.3.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run6/gila-trout.stru_r6.3.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4607182420492729603
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===========]
Number of iterations: 29

Least-square error: 121581.367862
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run6/gila-trout.stru_r6.3.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run6/gila-trout.stru_r6.3.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      3
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run6/gila-trout.stru_r6.3.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run6/gila-trout.stru_r6.3.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.535848
Cross-Entropy (masked data):     0.559135
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 4  repetition 6      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          4
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run6/gila-trout.stru_r6.4.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run6/gila-trout.stru_r6.4.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140202310155523
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===========]
Number of iterations: 30

Least-square error: 112346.663000
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run6/gila-trout.stru_r6.4.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run6/gila-trout.stru_r6.4.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      4
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run6/gila-trout.stru_r6.4.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run6/gila-trout.stru_r6.4.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.484245
Cross-Entropy (masked data):     0.517057
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 5  repetition 6      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          5
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run6/gila-trout.stru_r6.5.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run6/gila-trout.stru_r6.5.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140202310155523
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=========================]
Number of iterations: 67

Least-square error: 108524.054831
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run6/gila-trout.stru_r6.5.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run6/gila-trout.stru_r6.5.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      5
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run6/gila-trout.stru_r6.5.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run6/gila-trout.stru_r6.5.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.465314
Cross-Entropy (masked data):     0.511144
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 6  repetition 6      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          6
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run6/gila-trout.stru_r6.6.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run6/gila-trout.stru_r6.6.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140202310155523
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [====================]
Number of iterations: 53

Least-square error: 106983.968171
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run6/gila-trout.stru_r6.6.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run6/gila-trout.stru_r6.6.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      6
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run6/gila-trout.stru_r6.6.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run6/gila-trout.stru_r6.6.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.461538
Cross-Entropy (masked data):     0.511499
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 7  repetition 6      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          7
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run6/gila-trout.stru_r6.7.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run6/gila-trout.stru_r6.7.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140202310155523
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===============]
Number of iterations: 40

Least-square error: 103825.896247
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run6/gila-trout.stru_r6.7.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run6/gila-trout.stru_r6.7.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      7
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run6/gila-trout.stru_r6.7.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run6/gila-trout.stru_r6.7.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.445859
Cross-Entropy (masked data):     0.506032
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 8  repetition 6      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          8
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run6/gila-trout.stru_r6.8.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run6/gila-trout.stru_r6.8.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140202310155523
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=====================]
Number of iterations: 55

Least-square error: 102020.884421
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run6/gila-trout.stru_r6.8.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run6/gila-trout.stru_r6.8.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      8
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run6/gila-trout.stru_r6.8.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run6/gila-trout.stru_r6.8.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.436512
Cross-Entropy (masked data):     0.504002
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 9  repetition 6      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          9
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run6/gila-trout.stru_r6.9.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run6/gila-trout.stru_r6.9.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140202310155523
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [================]
Number of iterations: 43

Least-square error: 101034.603114
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run6/gila-trout.stru_r6.9.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run6/gila-trout.stru_r6.9.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      9
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run6/gila-trout.stru_r6.9.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run6/gila-trout.stru_r6.9.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.43159
Cross-Entropy (masked data):     0.506278
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 10  repetition 6      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          10
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run6/gila-trout.stru_r6.10.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run6/gila-trout.stru_r6.10.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140202310155523
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=====================]
Number of iterations: 56

Least-square error: 99112.670176
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run6/gila-trout.stru_r6.10.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run6/gila-trout.stru_r6.10.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      10
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run6/gila-trout.stru_r6.10.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run6/gila-trout.stru_r6.10.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.422761
Cross-Entropy (masked data):     0.507993
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] 1078367232
[1] "*************************************"
[1] "*          create.dataset            *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)                 154
        -L (number of loci)                        2381
        -s (seed random init)                      1078367232
        -r (percentage of masked data)             0.05
        -x (genotype file in .geno format)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -o (output file in .geno format)           /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno

 Write genotype file with masked data, /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.

[1] "*************************************"
[1] "* sNMF K = 2  repetition 7      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          2
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run7/gila-trout.stru_r7.2.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run7/gila-trout.stru_r7.2.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201695810560
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=================]
Number of iterations: 45

Least-square error: 134135.455299
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run7/gila-trout.stru_r7.2.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run7/gila-trout.stru_r7.2.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      2
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run7/gila-trout.stru_r7.2.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run7/gila-trout.stru_r7.2.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.60835
Cross-Entropy (masked data):     0.633878
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 3  repetition 7      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          3
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run7/gila-trout.stru_r7.3.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run7/gila-trout.stru_r7.3.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201695810560
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===============]
Number of iterations: 41

Least-square error: 121464.150039
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run7/gila-trout.stru_r7.3.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run7/gila-trout.stru_r7.3.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      3
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run7/gila-trout.stru_r7.3.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run7/gila-trout.stru_r7.3.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.535679
Cross-Entropy (masked data):     0.573493
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 4  repetition 7      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          4
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run7/gila-trout.stru_r7.4.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run7/gila-trout.stru_r7.4.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4611686019505755136
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 27

Least-square error: 112132.307403
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run7/gila-trout.stru_r7.4.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run7/gila-trout.stru_r7.4.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      4
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run7/gila-trout.stru_r7.4.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run7/gila-trout.stru_r7.4.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.483773
Cross-Entropy (masked data):     0.527106
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 5  repetition 7      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          5
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run7/gila-trout.stru_r7.5.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run7/gila-trout.stru_r7.5.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201695810560
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [============================]
Number of iterations: 74

Least-square error: 108412.273446
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run7/gila-trout.stru_r7.5.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run7/gila-trout.stru_r7.5.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      5
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run7/gila-trout.stru_r7.5.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run7/gila-trout.stru_r7.5.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.464964
Cross-Entropy (masked data):     0.513417
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 6  repetition 7      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          6
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run7/gila-trout.stru_r7.6.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run7/gila-trout.stru_r7.6.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201695810560
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=================================]
Number of iterations: 88

Least-square error: 105530.796541
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run7/gila-trout.stru_r7.6.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run7/gila-trout.stru_r7.6.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      6
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run7/gila-trout.stru_r7.6.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run7/gila-trout.stru_r7.6.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.450678
Cross-Entropy (masked data):     0.508192
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 7  repetition 7      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          7
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run7/gila-trout.stru_r7.7.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run7/gila-trout.stru_r7.7.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201695810560
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [================]
Number of iterations: 44

Least-square error: 103617.360410
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run7/gila-trout.stru_r7.7.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run7/gila-trout.stru_r7.7.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      7
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run7/gila-trout.stru_r7.7.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run7/gila-trout.stru_r7.7.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.445481
Cross-Entropy (masked data):     0.510624
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 8  repetition 7      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          8
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run7/gila-trout.stru_r7.8.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run7/gila-trout.stru_r7.8.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201695810560
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=================]
Number of iterations: 46

Least-square error: 102131.409154
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run7/gila-trout.stru_r7.8.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run7/gila-trout.stru_r7.8.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      8
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run7/gila-trout.stru_r7.8.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run7/gila-trout.stru_r7.8.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.437683
Cross-Entropy (masked data):     0.511496
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 9  repetition 7      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          9
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run7/gila-trout.stru_r7.9.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run7/gila-trout.stru_r7.9.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201695810560
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===============]
Number of iterations: 39

Least-square error: 100378.802283
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run7/gila-trout.stru_r7.9.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run7/gila-trout.stru_r7.9.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      9
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run7/gila-trout.stru_r7.9.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run7/gila-trout.stru_r7.9.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.429415
Cross-Entropy (masked data):     0.509714
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 10  repetition 7      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          10
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run7/gila-trout.stru_r7.10.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run7/gila-trout.stru_r7.10.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201695810560
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=====================]
Number of iterations: 55

Least-square error: 99132.991458
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run7/gila-trout.stru_r7.10.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run7/gila-trout.stru_r7.10.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      10
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run7/gila-trout.stru_r7.10.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run7/gila-trout.stru_r7.10.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.424086
Cross-Entropy (masked data):     0.513839
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] 526794664
[1] "*************************************"
[1] "*          create.dataset            *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)                 154
        -L (number of loci)                        2381
        -s (seed random init)                      526794664
        -r (percentage of masked data)             0.05
        -x (genotype file in .geno format)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -o (output file in .geno format)           /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno

 Write genotype file with masked data, /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.

[1] "*************************************"
[1] "* sNMF K = 2  repetition 8      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          2
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run8/gila-trout.stru_r8.2.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run8/gila-trout.stru_r8.2.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201144237992
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==============]
Number of iterations: 37

Least-square error: 134113.427939
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run8/gila-trout.stru_r8.2.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run8/gila-trout.stru_r8.2.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      2
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run8/gila-trout.stru_r8.2.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run8/gila-trout.stru_r8.2.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.608456
Cross-Entropy (masked data):     0.619609
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 3  repetition 8      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          3
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run8/gila-trout.stru_r8.3.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run8/gila-trout.stru_r8.3.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201144237992
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===============]
Number of iterations: 41

Least-square error: 121295.940212
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run8/gila-trout.stru_r8.3.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run8/gila-trout.stru_r8.3.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      3
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run8/gila-trout.stru_r8.3.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run8/gila-trout.stru_r8.3.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.535495
Cross-Entropy (masked data):     0.564114
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 4  repetition 8      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          4
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run8/gila-trout.stru_r8.4.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run8/gila-trout.stru_r8.4.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  1048498814888
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=========]
Number of iterations: 25

Least-square error: 112223.669809
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run8/gila-trout.stru_r8.4.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run8/gila-trout.stru_r8.4.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      4
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run8/gila-trout.stru_r8.4.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run8/gila-trout.stru_r8.4.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.484278
Cross-Entropy (masked data):     0.520997
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 5  repetition 8      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          5
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run8/gila-trout.stru_r8.5.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run8/gila-trout.stru_r8.5.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  526794664
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [======================]
Number of iterations: 59

Least-square error: 109043.403117
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run8/gila-trout.stru_r8.5.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run8/gila-trout.stru_r8.5.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      5
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run8/gila-trout.stru_r8.5.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run8/gila-trout.stru_r8.5.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.469275
Cross-Entropy (masked data):     0.513007
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 6  repetition 8      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          6
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run8/gila-trout.stru_r8.6.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run8/gila-trout.stru_r8.6.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4821761960
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [================]
Number of iterations: 44

Least-square error: 106599.523963
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run8/gila-trout.stru_r8.6.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run8/gila-trout.stru_r8.6.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      6
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run8/gila-trout.stru_r8.6.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run8/gila-trout.stru_r8.6.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.461148
Cross-Entropy (masked data):     0.511412
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 7  repetition 8      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          7
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run8/gila-trout.stru_r8.7.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run8/gila-trout.stru_r8.7.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201144237992
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [============]
Number of iterations: 32

Least-square error: 103614.792821
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run8/gila-trout.stru_r8.7.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run8/gila-trout.stru_r8.7.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      7
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run8/gila-trout.stru_r8.7.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run8/gila-trout.stru_r8.7.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.445169
Cross-Entropy (masked data):     0.506521
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 8  repetition 8      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          8
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run8/gila-trout.stru_r8.8.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run8/gila-trout.stru_r8.8.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4611686018954182568
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==================]
Number of iterations: 49

Least-square error: 101763.337991
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run8/gila-trout.stru_r8.8.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run8/gila-trout.stru_r8.8.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      8
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run8/gila-trout.stru_r8.8.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run8/gila-trout.stru_r8.8.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.43655
Cross-Entropy (masked data):     0.503425
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 9  repetition 8      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          9
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run8/gila-trout.stru_r8.9.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run8/gila-trout.stru_r8.9.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201144237992
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 28

Least-square error: 100690.371599
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run8/gila-trout.stru_r8.9.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run8/gila-trout.stru_r8.9.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      9
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run8/gila-trout.stru_r8.9.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run8/gila-trout.stru_r8.9.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.431425
Cross-Entropy (masked data):     0.506194
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 10  repetition 8      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          10
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run8/gila-trout.stru_r8.10.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run8/gila-trout.stru_r8.10.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201144237992
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 26

Least-square error: 98625.683667
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run8/gila-trout.stru_r8.10.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run8/gila-trout.stru_r8.10.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      10
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run8/gila-trout.stru_r8.10.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run8/gila-trout.stru_r8.10.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.420669
Cross-Entropy (masked data):     0.503427
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] 1266034765
[1] "*************************************"
[1] "*          create.dataset            *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)                 154
        -L (number of loci)                        2381
        -s (seed random init)                      1266034765
        -r (percentage of masked data)             0.05
        -x (genotype file in .geno format)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -o (output file in .geno format)           /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno

 Write genotype file with masked data, /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.

[1] "*************************************"
[1] "* sNMF K = 2  repetition 9      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          2
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run9/gila-trout.stru_r9.2.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run9/gila-trout.stru_r9.2.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201883478093
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=============]
Number of iterations: 35

Least-square error: 134007.946440
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run9/gila-trout.stru_r9.2.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run9/gila-trout.stru_r9.2.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      2
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run9/gila-trout.stru_r9.2.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run9/gila-trout.stru_r9.2.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.608236
Cross-Entropy (masked data):     0.630609
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 3  repetition 9      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          3
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run9/gila-trout.stru_r9.3.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run9/gila-trout.stru_r9.3.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4611686019693422669
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 27

Least-square error: 121397.657649
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run9/gila-trout.stru_r9.3.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run9/gila-trout.stru_r9.3.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      3
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run9/gila-trout.stru_r9.3.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run9/gila-trout.stru_r9.3.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.535479
Cross-Entropy (masked data):     0.568172
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 4  repetition 9      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          4
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run9/gila-trout.stru_r9.4.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run9/gila-trout.stru_r9.4.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201883478093
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 26

Least-square error: 112152.800068
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run9/gila-trout.stru_r9.4.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run9/gila-trout.stru_r9.4.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      4
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run9/gila-trout.stru_r9.4.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run9/gila-trout.stru_r9.4.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.48385
Cross-Entropy (masked data):     0.527675
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 5  repetition 9      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          5
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run9/gila-trout.stru_r9.5.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run9/gila-trout.stru_r9.5.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201883478093
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=====================]
Number of iterations: 56

Least-square error: 108331.872217
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run9/gila-trout.stru_r9.5.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run9/gila-trout.stru_r9.5.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      5
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run9/gila-trout.stru_r9.5.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run9/gila-trout.stru_r9.5.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.46495
Cross-Entropy (masked data):     0.517835
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 6  repetition 9      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          6
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run9/gila-trout.stru_r9.6.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run9/gila-trout.stru_r9.6.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201883478093
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=========================]
Number of iterations: 66

Least-square error: 105465.428921
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run9/gila-trout.stru_r9.6.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run9/gila-trout.stru_r9.6.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      6
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run9/gila-trout.stru_r9.6.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run9/gila-trout.stru_r9.6.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.450463
Cross-Entropy (masked data):     0.509917
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 7  repetition 9      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          7
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run9/gila-trout.stru_r9.7.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run9/gila-trout.stru_r9.7.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4611686019693422669
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===============]
Number of iterations: 39

Least-square error: 103416.406068
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run9/gila-trout.stru_r9.7.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run9/gila-trout.stru_r9.7.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      7
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run9/gila-trout.stru_r9.7.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run9/gila-trout.stru_r9.7.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.445228
Cross-Entropy (masked data):     0.512589
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 8  repetition 9      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          8
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run9/gila-trout.stru_r9.8.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run9/gila-trout.stru_r9.8.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201883478093
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==================]
Number of iterations: 48

Least-square error: 101876.537708
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run9/gila-trout.stru_r9.8.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run9/gila-trout.stru_r9.8.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      8
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run9/gila-trout.stru_r9.8.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run9/gila-trout.stru_r9.8.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.436259
Cross-Entropy (masked data):     0.512893
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 9  repetition 9      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          9
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run9/gila-trout.stru_r9.9.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run9/gila-trout.stru_r9.9.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201883478093
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [===================]
Number of iterations: 50

Least-square error: 100172.370218
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run9/gila-trout.stru_r9.9.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run9/gila-trout.stru_r9.9.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      9
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run9/gila-trout.stru_r9.9.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run9/gila-trout.stru_r9.9.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.429341
Cross-Entropy (masked data):     0.515309
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 10  repetition 9      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          10
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run9/gila-trout.stru_r9.10.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run9/gila-trout.stru_r9.10.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201883478093
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [============]
Number of iterations: 33

Least-square error: 98865.475852
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run9/gila-trout.stru_r9.10.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run9/gila-trout.stru_r9.10.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      10
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run9/gila-trout.stru_r9.10.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run9/gila-trout.stru_r9.10.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.423882
Cross-Entropy (masked data):     0.511868
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] 1338407366
[1] "*************************************"
[1] "*          create.dataset            *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)                 154
        -L (number of loci)                        2381
        -s (seed random init)                      1338407366
        -r (percentage of masked data)             0.05
        -x (genotype file in .geno format)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -o (output file in .geno format)           /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno

 Write genotype file with masked data, /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.

[1] "*************************************"
[1] "* sNMF K = 2  repetition 10      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          2
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run10/gila-trout.stru_r10.2.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run10/gila-trout.stru_r10.2.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201955850694
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==============]
Number of iterations: 37

Least-square error: 133899.252105
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run10/gila-trout.stru_r10.2.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run10/gila-trout.stru_r10.2.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      2
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run10/gila-trout.stru_r10.2.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K2/run10/gila-trout.stru_r10.2.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.608222
Cross-Entropy (masked data):     0.625256
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 3  repetition 10      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          3
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run10/gila-trout.stru_r10.3.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run10/gila-trout.stru_r10.3.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201955850694
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [=============]
Number of iterations: 34

Least-square error: 121340.504539
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run10/gila-trout.stru_r10.3.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run10/gila-trout.stru_r10.3.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      3
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run10/gila-trout.stru_r10.3.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K3/run10/gila-trout.stru_r10.3.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.535952
Cross-Entropy (masked data):     0.560691
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 4  repetition 10      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          4
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run10/gila-trout.stru_r10.4.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run10/gila-trout.stru_r10.4.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201955850694
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 28

Least-square error: 112147.274067
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run10/gila-trout.stru_r10.4.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run10/gila-trout.stru_r10.4.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      4
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run10/gila-trout.stru_r10.4.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K4/run10/gila-trout.stru_r10.4.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.484131
Cross-Entropy (masked data):     0.520412
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 5  repetition 10      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          5
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run10/gila-trout.stru_r10.5.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run10/gila-trout.stru_r10.5.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201955850694
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [============]
Number of iterations: 33

Least-square error: 109084.550243
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run10/gila-trout.stru_r10.5.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run10/gila-trout.stru_r10.5.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      5
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run10/gila-trout.stru_r10.5.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K5/run10/gila-trout.stru_r10.5.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.469318
Cross-Entropy (masked data):     0.510202
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 6  repetition 10      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          6
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run10/gila-trout.stru_r10.6.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run10/gila-trout.stru_r10.6.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4652521881621395910
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [========================]
Number of iterations: 63

Least-square error: 105566.462514
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run10/gila-trout.stru_r10.6.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run10/gila-trout.stru_r10.6.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      6
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run10/gila-trout.stru_r10.6.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K6/run10/gila-trout.stru_r10.6.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.450561
Cross-Entropy (masked data):     0.501374
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 7  repetition 10      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          7
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run10/gila-trout.stru_r10.7.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run10/gila-trout.stru_r10.7.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201955850694
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [====================]
Number of iterations: 53

Least-square error: 103902.536833
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run10/gila-trout.stru_r10.7.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run10/gila-trout.stru_r10.7.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      7
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run10/gila-trout.stru_r10.7.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K7/run10/gila-trout.stru_r10.7.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.446097
Cross-Entropy (masked data):     0.504445
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 8  repetition 10      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          8
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run10/gila-trout.stru_r10.8.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run10/gila-trout.stru_r10.8.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201955850694
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========================================================]
Number of iterations: 156

Least-square error: 101980.425763
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run10/gila-trout.stru_r10.8.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run10/gila-trout.stru_r10.8.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      8
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run10/gila-trout.stru_r10.8.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K8/run10/gila-trout.stru_r10.8.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.436582
Cross-Entropy (masked data):     0.50552
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 9  repetition 10      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          9
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run10/gila-trout.stru_r10.9.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run10/gila-trout.stru_r10.9.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  4652521881621395910
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [==========]
Number of iterations: 28

Least-square error: 100853.282064
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run10/gila-trout.stru_r10.9.Q:       OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run10/gila-trout.stru_r10.9.G:    OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      9
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run10/gila-trout.stru_r10.9.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K9/run10/gila-trout.stru_r10.9.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.43386
Cross-Entropy (masked data):     0.506182
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

[1] "*************************************"
[1] "* sNMF K = 10  repetition 10      *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)             154
        -L (number of loci)                    2381
        -K (number of ancestral pops)          10
        -x (input file)                        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        -q (individual admixture file)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run10/gila-trout.stru_r10.10.Q
        -g (ancestral frequencies file)        /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run10/gila-trout.stru_r10.10.G
        -i (number max of iterations)          200
        -a (regularization parameter)          10
        -s (seed random init)                  140201955850694
        -e (tolerance error)                   1E-05
        -p (number of processes)               1
        - diploid

Read genotype file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno:      OK.


Main algorithm:
    [                                                                           ]
    [====================]
Number of iterations: 54

Least-square error: 99293.550694
Write individual ancestry coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run10/gila-trout.stru_r10.10.Q:     OK.
Write ancestral allele frequency coefficient file /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run10/gila-trout.stru_r10.10.G:  OK.

[1] "*************************************"
[1] "*    cross-entropy estimation       *"
[1] "*************************************"
summary of the options:

        -n (number of individuals)         154
        -L (number of loci)                2381
        -K (number of ancestral pops)      10
        -x (genotype file)                 /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.geno
        -q (individual admixture)          /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run10/gila-trout.stru_r10.10.Q
        -g (ancestral frequencies)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/K10/run10/gila-trout.stru_r10.10.G
        -i (with masked genotypes)         /Users/kent/Documents/EEB-348/Lecture-Notes-in-Population-Genetics/Labs/gila-trout.stru.snmf/masked/gila-trout.stru_I.geno
        - diploid

Cross-Entropy (all data):    0.424468
Cross-Entropy (masked data):     0.507231
The project is saved into :
 gila-trout.stru.snmfProject 

To load the project, use:
 project = load.snmfProject("gila-trout.stru.snmfProject")

To remove the project, use:
 remove.snmfProject("gila-trout.stru.snmfProject")

I’m going to save the results in an .Rsave file. That’s what I’ll give you, so that you can load it and use the results as if you’d run snmf() yourself.

save(trout, file = "trout.Rsave")

Then I zipped all of the files in the gila-trout.stru.snmf directory.