plink质控及转换文件、admixture软件学习记录

plink质控及转换文件、admixture软件学习记录

非vcf文件，可按照以下两个文件格式转换数据，再进行后续分析。

ped文件格式：

map文件格式：

有坑：admixture似乎不能识别非整数形式的染色体名,所以染色体命名最好以整数形式。

 ADMIXTURE Version 1.3.0 Copyright 2008-2015 David Alexander, Suyash Shringarpure, John Novembre, Ken Lange Please cite our paper! Information at www.genetics.ucla.edu/software/admixture Cross-validation will be performed. Folds=5. Random seed: 43 Point estimation method: Block relaxation algorithm Convergence acceleration algorithm: QuasiNewton, 3 secant conditions Point estimation will terminate when objective function delta < 0.0001 Estimation of standard errors disabled; will compute point estimates only. Invalid chromosome code! Use integers. 

第二列：SNP等 变异名称，不重要，直接设为 . 。
第三列：SNP的摩尔位置，不重要，未知可设为0。
第四列：变异位点物理坐标：int数字。

一. 安装admixture

# 安装： wget http://dalexander.github.io/admixture/binaries/admixture_linux-1.3.0.tar.gz # 解压 [yanglv@localhost software]$ tar -zxvf admixture_linux-1.3.0.tar.gz dist/admixture_linux-1.3.0/ dist/admixture_linux-1.3.0/README.32.txt dist/admixture_linux-1.3.0/admixture dist/admixture_linux-1.3.0/admixture32 dist/admixture_linux-1.3.0/admixture-manual.pdf /home/yanglv/software/dist/admixture_linux-1.3.0/admixture  ADMIXTURE Version 1.3.0   Copyright 2008-2015   David Alexander, Suyash Shringarpure,   John Novembre, Ken Lange     Please cite our paper!   Information at www.genetics.ucla.edu/software/admixture  Usage: admixture <input file> <K> See --help or manual for more advanced usage. 

不需要安装，解压即用。

二：plink 问题记录

生成map和ped文件后，用plink质控和转换格式，遇到问题：

plink -noweb --file admixture_test2 --geno 0.05 --maf 0.05 --hwe 0.0001 --make-bed --allow-extra-chr --out admixture_test2 PLINK v1.90b6.12 64-bit (28 Oct 2019) www.cog-genomics.org/plink/1.9/ (C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to admixture/admixture_test2.log. Options in effect: --allow-extra-chr --file admixture_test2 --geno 0.05 --hwe 0.0001 --maf 0.05 --make-bed --noweb --out admixture_test2 Note: --noweb has no effect since no web check is implemented yet.  MB RAM detected; reserving  MB for main workspace. Error: Invalid chromosome code '27' on line 30494 of .map file. (This is disallowed for humans. Check if the problem is with your data, or if you forgot to define a different chromosome set with e.g. --chr-set.) 

27好染色体不属于人类染色体而报错，即plink默认物质是人，加 --allow-extra-chr参数也会报错，改物种即可。加入参数--cow --dog --rice 等，可解决。

结果：admixture结果选择最小的CV

参考: GWAS 学习之admixture.

芜湖~

for K in 1 2 3 4 5 6 7 8;do /home/yanglv/software/dist/admixture_linux-1.3.0/admixture --cv /home/yanglv/soft_project/Target/target_result_test/admixture/admixture_test2.bed $K|tee log${K}.out;done [yanglv@localhost admixture]$ grep -h CV log*.out CV error (K=1): 0.39256 CV error (K=2): 0.31942 CV error (K=3): 0.31189 CV error (K=4): 0.30861 CV error (K=5): 0.30449 CV error (K=6): 0.29635 CV error (K=7): 0.29427 CV error (K=8): 0.29474 

记录

[yanglv@localhost admixture]$ for K in 1 2 3 4 5 6 7 8;do /home/yanglv/software/dist/admixture_linux-1.3.0/admixture --cv /home/yanglv/soft_project/Target/target_result_test/admixture/admixture_test2.bed $K|tee log${K}.out;done ADMIXTURE Version 1.3.0 Copyright 2008-2015 David Alexander, Suyash Shringarpure, John Novembre, Ken Lange Please cite our paper! Information at www.genetics.ucla.edu/software/admixture Cross-validation will be performed. Folds=5. Random seed: 43 Point estimation method: Block relaxation algorithm Convergence acceleration algorithm: QuasiNewton, 3 secant conditions Point estimation will terminate when objective function delta < 0.0001 Estimation of standard errors disabled; will compute point estimates only. Size of G: 719x1068 Performing five EM steps to prime main algorithm 1 (EM) Elapsed: 0.035 Loglikelihood: - (delta): 1.02505e+06 2 (EM) Elapsed: 0.017 Loglikelihood: - (delta): 0 3 (EM) Elapsed: 0.016 Loglikelihood: - (delta): 0 4 (EM) Elapsed: 0.016 Loglikelihood: - (delta): 0 5 (EM) Elapsed: 0.017 Loglikelihood: - (delta): 0 Initial loglikelihood: - Starting main algorithm 1 (QN/Block) Elapsed: 0.067 Loglikelihood: - (delta): 0 Summary: Converged in 1 iterations (0.273 sec) Loglikelihood: -. CV error (K=1): 0.39256 Writing output files. ADMIXTURE Version 1.3.0 Copyright 2008-2015 David Alexander, Suyash Shringarpure, John Novembre, Ken Lange Please cite our paper! Information at www.genetics.ucla.edu/software/admixture Cross-validation will be performed. Folds=5. Random seed: 43 Point estimation method: Block relaxation algorithm Convergence acceleration algorithm: QuasiNewton, 3 secant conditions Point estimation will terminate when objective function delta < 0.0001 Estimation of standard errors disabled; will compute point estimates only. Size of G: 719x1068 Performing five EM steps to prime main algorithm 1 (EM) Elapsed: 0.029 Loglikelihood: - (delta):  2 (EM) Elapsed: 0.029 Loglikelihood: - (delta): 20019 3 (EM) Elapsed: 0.029 Loglikelihood: - (delta): 3267.52 4 (EM) Elapsed: 0.029 Loglikelihood: - (delta): 1515.85 5 (EM) Elapsed: 0.029 Loglikelihood: - (delta): 831.844 Initial loglikelihood: - Starting main algorithm 1 (QN/Block) Elapsed: 0.069 Loglikelihood: - (delta): 28323.5 2 (QN/Block) Elapsed: 0.069 Loglikelihood: - (delta): 15987.8 3 (QN/Block) Elapsed: 0.083 Loglikelihood: - (delta): 8610.58 4 (QN/Block) Elapsed: 0.107 Loglikelihood: - (delta): 3134.31 5 (QN/Block) Elapsed: 0.181 Loglikelihood: - (delta): 557.027 6 (QN/Block) Elapsed: 0.086 Loglikelihood: - (delta): 9.20631 7 (QN/Block) Elapsed: 0.082 Loglikelihood: - (delta): 0. 8 (QN/Block) Elapsed: 0.126 Loglikelihood: - (delta): 0.0 9 (QN/Block) Elapsed: 0.098 Loglikelihood: - (delta): 0.0 10 (QN/Block) Elapsed: 0.121 Loglikelihood: - (delta): 0.000 11 (QN/Block) Elapsed: 0.087 Loglikelihood: - (delta): 0.000 12 (QN/Block) Elapsed: 0.087 Loglikelihood: - (delta): 2.83706e-05 Summary: Converged in 12 iterations (1.491 sec) Loglikelihood: -. Fst divergences between estimated populations: Pop0 Pop0 Pop1 0.148 CV error (K=2): 0.31942 Writing output files. ADMIXTURE Version 1.3.0 Copyright 2008-2015 David Alexander, Suyash Shringarpure, John Novembre, Ken Lange Please cite our paper! Information at www.genetics.ucla.edu/software/admixture Cross-validation will be performed. Folds=5. Random seed: 43 Point estimation method: Block relaxation algorithm Convergence acceleration algorithm: QuasiNewton, 3 secant conditions Point estimation will terminate when objective function delta < 0.0001 Estimation of standard errors disabled; will compute point estimates only. Size of G: 719x1068 Performing five EM steps to prime main algorithm 1 (EM) Elapsed: 0.041 Loglikelihood: - (delta):  2 (EM) Elapsed: 0.041 Loglikelihood: - (delta): 26965.1 3 (EM) Elapsed: 0.041 Loglikelihood: - (delta): 4935.7 4 (EM) Elapsed: 0.041 Loglikelihood: - (delta): 2319.15 5 (EM) Elapsed: 0.041 Loglikelihood: - (delta): 1495.4 Initial loglikelihood: - Starting main algorithm 1 (QN/Block) Elapsed: 0.098 Loglikelihood: - (delta): 41990.2 2 (QN/Block) Elapsed: 0.098 Loglikelihood: - (delta): 12784.6 3 (QN/Block) Elapsed: 0.112 Loglikelihood: - (delta): 6757.89 4 (QN/Block) Elapsed: 0.127 Loglikelihood: - (delta): 2415.83 5 (QN/Block) Elapsed: 0.143 Loglikelihood: - (delta): 232.638 6 (QN/Block) Elapsed: 0.119 Loglikelihood: - (delta): 46.0302 7 (QN/Block) Elapsed: 0.133 Loglikelihood: - (delta): 27.7845 8 (QN/Block) Elapsed: 0.137 Loglikelihood: - (delta): 17.4421 9 (QN/Block) Elapsed: 0.136 Loglikelihood: - (delta): 31.2034 10 (QN/Block) Elapsed: 0.138 Loglikelihood: - (delta): 46.2003 11 (QN/Block) Elapsed: 0.194 Loglikelihood: - (delta): 75.5179 12 (QN/Block) Elapsed: 0.171 Loglikelihood: - (delta): 77.7136 13 (QN/Block) Elapsed: 0.163 Loglikelihood: - (delta): 86.7648 14 (QN/Block) Elapsed: 0.137 Loglikelihood: - (delta): 119.312 15 (QN/Block) Elapsed: 0.128 Loglikelihood: - (delta): 32.5818 16 (QN/Block) Elapsed: 0.127 Loglikelihood: - (delta): 6.40741 17 (QN/Block) Elapsed: 0.112 Loglikelihood: - (delta): 3.91217 18 (QN/Block) Elapsed: 0.127 Loglikelihood: - (delta): 1.69153 19 (QN/Block) Elapsed: 0.112 Loglikelihood: - (delta): 0. 20 (QN/Block) Elapsed: 0.112 Loglikelihood: - (delta): 0.0 21 (QN/Block) Elapsed: 0.126 Loglikelihood: - (delta): 0.00 22 (QN/Block) Elapsed: 0.121 Loglikelihood: - (delta): 0.00 23 (QN/Block) Elapsed: 0.113 Loglikelihood: - (delta): 0.00 24 (QN/Block) Elapsed: 0.136 Loglikelihood: - (delta): 0.0052317 25 (QN/Block) Elapsed: 0.137 Loglikelihood: - (delta): 0.00 26 (QN/Block) Elapsed: 0.119 Loglikelihood: - (delta): 0.0 27 (QN/Block) Elapsed: 0.133 Loglikelihood: - (delta): 0.0 28 (QN/Block) Elapsed: 0.133 Loglikelihood: - (delta): 5.01985e-05 Summary: Converged in 28 iterations (4.14 sec) Loglikelihood: -. Fst divergences between estimated populations: Pop0 Pop1 Pop0 Pop1 0.153 Pop2 0.173 0.067 CV error (K=3): 0.31189 Writing output files. ADMIXTURE Version 1.3.0 Copyright 2008-2015 David Alexander, Suyash Shringarpure, John Novembre, Ken Lange Please cite our paper! Information at www.genetics.ucla.edu/software/admixture Cross-validation will be performed. Folds=5. Random seed: 43 Point estimation method: Block relaxation algorithm Convergence acceleration algorithm: QuasiNewton, 3 secant conditions Point estimation will terminate when objective function delta < 0.0001 Estimation of standard errors disabled; will compute point estimates only. Size of G: 719x1068 Performing five EM steps to prime main algorithm 1 (EM) Elapsed: 0.062 Loglikelihood: - (delta):  2 (EM) Elapsed: 0.064 Loglikelihood: - (delta): 28413.3 3 (EM) Elapsed: 0.071 Loglikelihood: - (delta): 5027.77 4 (EM) Elapsed: 0.073 Loglikelihood: - (delta): 2368.45 5 (EM) Elapsed: 0.055 Loglikelihood: - (delta): 1563.63 Initial loglikelihood: - Starting main algorithm 1 (QN/Block) Elapsed: 0.157 Loglikelihood: - (delta): 45571.5 2 (QN/Block) Elapsed: 0.153 Loglikelihood: - (delta): 13218.3 3 (QN/Block) Elapsed: 0.196 Loglikelihood: - (delta): 5309.76 4 (QN/Block) Elapsed: 0.211 Loglikelihood: - (delta): 3613.25 5 (QN/Block) Elapsed: 0.169 Loglikelihood: - (delta): 626.831 6 (QN/Block) Elapsed: 0.163 Loglikelihood: - (delta): 263.926 7 (QN/Block) Elapsed: 0.154 Loglikelihood: - (delta): 223.612 8 (QN/Block) Elapsed: 0.163 Loglikelihood: - (delta): 114.138 9 (QN/Block) Elapsed: 0.155 Loglikelihood: - (delta): 82.1681 10 (QN/Block) Elapsed: 0.179 Loglikelihood: - (delta): 217.032 11 (QN/Block) Elapsed: 0.178 Loglikelihood: - (delta): 244.291 12 (QN/Block) Elapsed: 0.178 Loglikelihood: - (delta): 183.086 13 (QN/Block) Elapsed: 0.184 Loglikelihood: - (delta): 61.1443 14 (QN/Block) Elapsed: 0.231 Loglikelihood: - (delta): 19.669 15 (QN/Block) Elapsed: 0.191 Loglikelihood: - (delta): 4.4163 16 (QN/Block) Elapsed: 0.183 Loglikelihood: - (delta): 1.65863 17 (QN/Block) Elapsed: 0.165 Loglikelihood: - (delta): 0. 18 (QN/Block) Elapsed: 0.176 Loglikelihood: - (delta): 0. 19 (QN/Block) Elapsed: 0.171 Loglikelihood: - (delta): 0.0 20 (QN/Block) Elapsed: 0.194 Loglikelihood: - (delta): 0.0 21 (QN/Block) Elapsed: 0.163 Loglikelihood: - (delta): 0.00 22 (QN/Block) Elapsed: 0.171 Loglikelihood: - (delta): 0.00 23 (QN/Block) Elapsed: 0.164 Loglikelihood: - (delta): 0.000 24 (QN/Block) Elapsed: 0.158 Loglikelihood: - (delta): 7.24026e-05 Summary: Converged in 24 iterations (4.813 sec) Loglikelihood: -.096272 Fst divergences between estimated populations: Pop0 Pop1 Pop2 Pop0 Pop1 0.241 Pop2 0.217 0.067 Pop3 0.102 0.166 0.149 CV error (K=4): 0.30861 Writing output files. ADMIXTURE Version 1.3.0 Copyright 2008-2015 David Alexander, Suyash Shringarpure, John Novembre, Ken Lange Please cite our paper! Information at www.genetics.ucla.edu/software/admixture Cross-validation will be performed. Folds=5. Random seed: 43 Point estimation method: Block relaxation algorithm Convergence acceleration algorithm: QuasiNewton, 3 secant conditions Point estimation will terminate when objective function delta < 0.0001 Estimation of standard errors disabled; will compute point estimates only. Size of G: 719x1068 Performing five EM steps to prime main algorithm 1 (EM) Elapsed: 0.089 Loglikelihood: - (delta):  2 (EM) Elapsed: 0.069 Loglikelihood: - (delta): 29633.7 3 (EM) Elapsed: 0.079 Loglikelihood: - (delta): 5552.37 4 (EM) Elapsed: 0.086 Loglikelihood: - (delta): 2631.87 5 (EM) Elapsed: 0.068 Loglikelihood: - (delta): 1774.9 Initial loglikelihood: - Starting main algorithm 1 (QN/Block) Elapsed: 0.2 Loglikelihood: - (delta): 48791.4 2 (QN/Block) Elapsed: 0.195 Loglikelihood: - (delta): 13006.4 3 (QN/Block) Elapsed: 0.224 Loglikelihood: - (delta): 5153.74 4 (QN/Block) Elapsed: 0.222 Loglikelihood: - (delta): 2892.42 5 (QN/Block) Elapsed: 0.22 Loglikelihood: - (delta): 1887.61 6 (QN/Block) Elapsed: 0.211 Loglikelihood: - (delta): 1500.98 7 (QN/Block) Elapsed: 0.206 Loglikelihood: - (delta): 884.311 8 (QN/Block) Elapsed: 0.213 Loglikelihood: - (delta): 430.537 9 (QN/Block) Elapsed: 0.212 Loglikelihood: - (delta): 149.84 10 (QN/Block) Elapsed: 0.208 Loglikelihood: - (delta): 54.5231 11 (QN/Block) Elapsed: 0.205 Loglikelihood: - (delta): 12.5922 12 (QN/Block) Elapsed: 0.212 Loglikelihood: - (delta): 3.30675 13 (QN/Block) Elapsed: 0.237 Loglikelihood: - (delta): 1.00734 14 (QN/Block) Elapsed: 0.245 Loglikelihood: - (delta): 0. 15 (QN/Block) Elapsed: 0.215 Loglikelihood: - (delta): 0.0 16 (QN/Block) Elapsed: 0.257 Loglikelihood: - (delta): 0.0 17 (QN/Block) Elapsed: 0.205 Loglikelihood: - (delta): 0.0075792 18 (QN/Block) Elapsed: 0.242 Loglikelihood: - (delta): 0.00 19 (QN/Block) Elapsed: 0.236 Loglikelihood: - (delta): 0.0010454 20 (QN/Block) Elapsed: 0.245 Loglikelihood: - (delta): 0.000 21 (QN/Block) Elapsed: 0.235 Loglikelihood: - (delta): 0.000 22 (QN/Block) Elapsed: 0.235 Loglikelihood: - (delta): 0.00013889 23 (QN/Block) Elapsed: 0.284 Loglikelihood: - (delta): 2.45788e-06 Summary: Converged in 23 iterations (5.855 sec) Loglikelihood: -. Fst divergences between estimated populations: Pop0 Pop1 Pop2 Pop3 Pop0 Pop1 0.099 Pop2 0.100 0.107 Pop3 0.181 0.181 0.180 Pop4 0.082 0.091 0.086 0.169 CV error (K=5): 0.30449 Writing output files. ADMIXTURE Version 1.3.0 Copyright 2008-2015 David Alexander, Suyash Shringarpure, John Novembre, Ken Lange Please cite our paper! Information at www.genetics.ucla.edu/software/admixture Cross-validation will be performed. Folds=5. Random seed: 43 Point estimation method: Block relaxation algorithm Convergence acceleration algorithm: QuasiNewton, 3 secant conditions Point estimation will terminate when objective function delta < 0.0001 Estimation of standard errors disabled; will compute point estimates only. Size of G: 719x1068 Performing five EM steps to prime main algorithm 1 (EM) Elapsed: 0.143 Loglikelihood: - (delta):  2 (EM) Elapsed: 0.086 Loglikelihood: - (delta): 30672.4 3 (EM) Elapsed: 0.086 Loglikelihood: - (delta): 5388.31 4 (EM) Elapsed: 0.086 Loglikelihood: - (delta): 2744.2 5 (EM) Elapsed: 0.086 Loglikelihood: - (delta): 1998.2 Initial loglikelihood: - Starting main algorithm 1 (QN/Block) Elapsed: 0.237 Loglikelihood: - (delta): 56389.4 2 (QN/Block) Elapsed: 0.237 Loglikelihood: - (delta): 12865.6 3 (QN/Block) Elapsed: 0.262 Loglikelihood: - (delta): 5613.42 4 (QN/Block) Elapsed: 0.289 Loglikelihood: - (delta): 2815.53 5 (QN/Block) Elapsed: 0.398 Loglikelihood: - (delta): 880.433 6 (QN/Block) Elapsed: 0.298 Loglikelihood: - (delta): 388.278 7 (QN/Block) Elapsed: 0.316 Loglikelihood: - (delta): 830.789 8 (QN/Block) Elapsed: 0.282 Loglikelihood: - (delta): 1122.85 9 (QN/Block) Elapsed: 0.365 Loglikelihood: - (delta): 405.81 10 (QN/Block) Elapsed: 0.288 Loglikelihood: - (delta): 251.812 11 (QN/Block) Elapsed: 0.291 Loglikelihood: - (delta): 69.4077 12 (QN/Block) Elapsed: 0.332 Loglikelihood: - (delta): 34.5988 13 (QN/Block) Elapsed: 0.273 Loglikelihood: - (delta): 17.2135 14 (QN/Block) Elapsed: 0.268 Loglikelihood: - (delta): 4.76113 15 (QN/Block) Elapsed: 0.273 Loglikelihood: - (delta): 0. 16 (QN/Block) Elapsed: 0.269 Loglikelihood: - (delta): 0. 17 (QN/Block) Elapsed: 0.268 Loglikelihood: - (delta): 0.0 18 (QN/Block) Elapsed: 0.289 Loglikelihood: - (delta): 0.00 19 (QN/Block) Elapsed: 0.282 Loglikelihood: - (delta): 0.000 20 (QN/Block) Elapsed: 0.271 Loglikelihood: - (delta): 1.53444e-05 Summary: Converged in 20 iterations (6.562 sec) Loglikelihood: -. Fst divergences between estimated populations: Pop0 Pop1 Pop2 Pop3 Pop4 Pop0 Pop1 0.158 Pop2 0.103 0.228 Pop3 0.175 0.087 0.242 Pop4 0.194 0.105 0.266 0.121 Pop5 0.187 0.108 0.262 0.129 0.136 CV error (K=6): 0.29635 Writing output files. ADMIXTURE Version 1.3.0 Copyright 2008-2015 David Alexander, Suyash Shringarpure, John Novembre, Ken Lange Please cite our paper! Information at www.genetics.ucla.edu/software/admixture Cross-validation will be performed. Folds=5. Random seed: 43 Point estimation method: Block relaxation algorithm Convergence acceleration algorithm: QuasiNewton, 3 secant conditions Point estimation will terminate when objective function delta < 0.0001 Estimation of standard errors disabled; will compute point estimates only. Size of G: 719x1068 Performing five EM steps to prime main algorithm 1 (EM) Elapsed: 0.106 Loglikelihood: - (delta):  2 (EM) Elapsed: 0.112 Loglikelihood: - (delta): 31270.2 3 (EM) Elapsed: 0.118 Loglikelihood: - (delta): 5230.35 4 (EM) Elapsed: 0.116 Loglikelihood: - (delta): 2654.37 5 (EM) Elapsed: 0.122 Loglikelihood: - (delta): 1996.6 Initial loglikelihood: - Starting main algorithm 1 (QN/Block) Elapsed: 0.294 Loglikelihood: - (delta): 60746.2 2 (QN/Block) Elapsed: 0.317 Loglikelihood: - (delta): 13774.7 3 (QN/Block) Elapsed: 0.328 Loglikelihood: - (delta): 5132.8 4 (QN/Block) Elapsed: 0.335 Loglikelihood: - (delta): 3304.89 5 (QN/Block) Elapsed: 0.317 Loglikelihood: - (delta): 918.535 6 (QN/Block) Elapsed: 0.317 Loglikelihood: - (delta): 373.719 7 (QN/Block) Elapsed: 0.326 Loglikelihood: - (delta): 162.206 8 (QN/Block) Elapsed: 0.318 Loglikelihood: - (delta): 72.875 9 (QN/Block) Elapsed: 0.318 Loglikelihood: - (delta): 17.3363 10 (QN/Block) Elapsed: 0.432 Loglikelihood: - (delta): 4.0415 11 (QN/Block) Elapsed: 0.404 Loglikelihood: - (delta): 1.29983 12 (QN/Block) Elapsed: 0.471 Loglikelihood: - (delta): 1.80102 13 (QN/Block) Elapsed: 0.383 Loglikelihood: - (delta): 1.50387 14 (QN/Block) Elapsed: 0.451 Loglikelihood: - (delta): 2.51678 15 (QN/Block) Elapsed: 0.351 Loglikelihood: - (delta): 4.83349 16 (QN/Block) Elapsed: 0.391 Loglikelihood: - (delta): 9.20407 17 (QN/Block) Elapsed: 0.492 Loglikelihood: - (delta): 7.66689 18 (QN/Block) Elapsed: 0.378 Loglikelihood: - (delta): 3.1878 19 (QN/Block) Elapsed: 0.462 Loglikelihood: - (delta): 2.25449 20 (QN/Block) Elapsed: 0.358 Loglikelihood: - (delta): 2.39676 21 (QN/Block) Elapsed: 0.386 Loglikelihood: - (delta): 0. 22 (QN/Block) Elapsed: 0.388 Loglikelihood: - (delta): 0.0 23 (QN/Block) Elapsed: 0.35 Loglikelihood: - (delta): 0.00 24 (QN/Block) Elapsed: 0.316 Loglikelihood: - (delta): 0.000 25 (QN/Block) Elapsed: 0.329 Loglikelihood: - (delta): 9.88959e-05 Summary: Converged in 25 iterations (10.148 sec) Loglikelihood: -. Fst divergences between estimated populations: Pop0 Pop1 Pop2 Pop3 Pop4 Pop5 Pop0 Pop1 0.180 Pop2 0.265 0.113 Pop3 0.161 0.191 0.284 Pop4 0.166 0.199 0.289 0.142 Pop5 0.124 0.166 0.255 0.114 0.112 Pop6 0.147 0.182 0.267 0.134 0.128 0.095 CV error (K=7): 0.29427 Writing output files. ADMIXTURE Version 1.3.0 Copyright 2008-2015 David Alexander, Suyash Shringarpure, John Novembre, Ken Lange Please cite our paper! Information at www.genetics.ucla.edu/software/admixture Cross-validation will be performed. Folds=5. Random seed: 43 Point estimation method: Block relaxation algorithm Convergence acceleration algorithm: QuasiNewton, 3 secant conditions Point estimation will terminate when objective function delta < 0.0001 Estimation of standard errors disabled; will compute point estimates only. Size of G: 719x1068 Performing five EM steps to prime main algorithm 1 (EM) Elapsed: 0.157 Loglikelihood: - (delta):  2 (EM) Elapsed: 0.123 Loglikelihood: - (delta): 31999.3 3 (EM) Elapsed: 0.124 Loglikelihood: - (delta): 4964.91 4 (EM) Elapsed: 0.172 Loglikelihood: - (delta): 2516.34 5 (EM) Elapsed: 0.146 Loglikelihood: - (delta): 1939.09 Initial loglikelihood: - Starting main algorithm 1 (QN/Block) Elapsed: 0.393 Loglikelihood: - (delta): 64115.3 2 (QN/Block) Elapsed: 0.392 Loglikelihood: - (delta): 14337.7 3 (QN/Block) Elapsed: 0.394 Loglikelihood: - (delta): 4852.03 4 (QN/Block) Elapsed: 0.396 Loglikelihood: - (delta): 2203.95 5 (QN/Block) Elapsed: 0.48 Loglikelihood: - (delta): 487.912 6 (QN/Block) Elapsed: 0.473 Loglikelihood: - (delta): 188.121 7 (QN/Block) Elapsed: 0.427 Loglikelihood: - (delta): 107.61 8 (QN/Block) Elapsed: 0.396 Loglikelihood: - (delta): 42.7561 9 (QN/Block) Elapsed: 0.415 Loglikelihood: - (delta): 29.4542 10 (QN/Block) Elapsed: 0.397 Loglikelihood: - (delta): 7.1703 11 (QN/Block) Elapsed: 0.453 Loglikelihood: - (delta): 2.94505 12 (QN/Block) Elapsed: 0.409 Loglikelihood: - (delta): 2.3553 13 (QN/Block) Elapsed: 0.466 Loglikelihood: - (delta): 1.80055 14 (QN/Block) Elapsed: 0.495 Loglikelihood: - (delta): 1.81308 15 (QN/Block) Elapsed: 0.468 Loglikelihood: - (delta): 2.86907 16 (QN/Block) Elapsed: 0.439 Loglikelihood: - (delta): 3.81053 17 (QN/Block) Elapsed: 0.425 Loglikelihood: - (delta): 5.71111 18 (QN/Block) Elapsed: 0.404 Loglikelihood: - (delta): 1.89774 19 (QN/Block) Elapsed: 0.416 Loglikelihood: - (delta): 6.10536 20 (QN/Block) Elapsed: 0.429 Loglikelihood: - (delta): 2.35111 21 (QN/Block) Elapsed: 0.39 Loglikelihood: - (delta): 1.00534 22 (QN/Block) Elapsed: 0.44 Loglikelihood: - (delta): 1.25458 23 (QN/Block) Elapsed: 0.563 Loglikelihood: - (delta): 0. 24 (QN/Block) Elapsed: 0.571 Loglikelihood: - (delta): 0.0 25 (QN/Block) Elapsed: 0.427 Loglikelihood: - (delta): 0.022227 26 (QN/Block) Elapsed: 0.388 Loglikelihood: - (delta): 0.0 27 (QN/Block) Elapsed: 0.401 Loglikelihood: - (delta): 0.00 28 (QN/Block) Elapsed: 0.401 Loglikelihood: - (delta): 0.00 29 (QN/Block) Elapsed: 0.405 Loglikelihood: - (delta): 0.000 30 (QN/Block) Elapsed: 0.412 Loglikelihood: - (delta): 0.000 31 (QN/Block) Elapsed: 0.442 Loglikelihood: - (delta): 0.000 32 (QN/Block) Elapsed: 0.433 Loglikelihood: - (delta): 0.000 33 (QN/Block) Elapsed: 0.552 Loglikelihood: - (delta): 0.000 34 (QN/Block) Elapsed: 0.451 Loglikelihood: - (delta): 0.000 35 (QN/Block) Elapsed: 0.432 Loglikelihood: - (delta): 0.000 36 (QN/Block) Elapsed: 0.445 Loglikelihood: - (delta): 0.000 37 (QN/Block) Elapsed: 0.426 Loglikelihood: - (delta): 0.000 38 (QN/Block) Elapsed: 0.453 Loglikelihood: - (delta): 0.00 39 (QN/Block) Elapsed: 0.478 Loglikelihood: - (delta): 0.0014087 40 (QN/Block) Elapsed: 0.416 Loglikelihood: - (delta): 0.0018823 41 (QN/Block) Elapsed: 0.424 Loglikelihood: - (delta): 0.00 42 (QN/Block) Elapsed: 0.483 Loglikelihood: - (delta): 0.00 43 (QN/Block) Elapsed: 0.445 Loglikelihood: - (delta): 0.00 44 (QN/Block) Elapsed: 0.43 Loglikelihood: - (delta): 0.00 45 (QN/Block) Elapsed: 0.465 Loglikelihood: - (delta): 0.00 46 (QN/Block) Elapsed: 0.423 Loglikelihood: - (delta): 0.0 47 (QN/Block) Elapsed: 0.427 Loglikelihood: - (delta): 0.0 48 (QN/Block) Elapsed: 0.427 Loglikelihood: - (delta): 0.019449 49 (QN/Block) Elapsed: 0.42 Loglikelihood: - (delta): 0.0 50 (QN/Block) Elapsed: 0.422 Loglikelihood: - (delta): 0.0 51 (QN/Block) Elapsed: 0.434 Loglikelihood: - (delta): 0.0 52 (QN/Block) Elapsed: 0.437 Loglikelihood: - (delta): 0.0 53 (QN/Block) Elapsed: 0.463 Loglikelihood: - (delta): 0.0 54 (QN/Block) Elapsed: 0.461 Loglikelihood: - (delta): 0.0 55 (QN/Block) Elapsed: 0.425 Loglikelihood: - (delta): 0.0 56 (QN/Block) Elapsed: 0.463 Loglikelihood: - (delta): 0.0 57 (QN/Block) Elapsed: 0.466 Loglikelihood: - (delta): 0.0 58 (QN/Block) Elapsed: 0.48 Loglikelihood: - (delta): 0.0 59 (QN/Block) Elapsed: 0.429 Loglikelihood: - (delta): 0.00 60 (QN/Block) Elapsed: 0.402 Loglikelihood: - (delta): 0.000 61 (QN/Block) Elapsed: 0.396 Loglikelihood: - (delta): 0.000 62 (QN/Block) Elapsed: 0.395 Loglikelihood: - (delta): 5.40009e-05 Summary: Converged in 62 iterations (28.651 sec) Loglikelihood: -. Fst divergences between estimated populations: Pop0 Pop1 Pop2 Pop3 Pop4 Pop5 Pop6 Pop0 Pop1 0.170 Pop2 0.218 0.096 Pop3 0.153 0.186 0.252 Pop4 0.150 0.194 0.250 0.138 Pop5 0.109 0.164 0.217 0.111 0.107 Pop6 0.258 0.130 0.125 0.285 0.289 0.257 Pop7 0.130 0.178 0.233 0.131 0.122 0.090 0.268 CV error (K=8): 0.29474 Writing output files.