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  1. /home/ubuntu/AdmixTools-master/bin/qpAdm: parameter file: qpAdm_parfile
  2. ### THE INPUT PARAMETERS
  3. ##PARAMETER NAME: VALUE
  4. indivname: /home/ubuntu/MainSet/robertDataset.ind
  5. snpname: /home/ubuntu/MainSet/robertDataset.snp
  6. genotypename: /home/ubuntu/MainSet/robertDataset.packedancestrymapgeno
  7. popleft: pleftA.txt
  8. popright: pRightC.tx
  9. fstatsoutname: fstats.tx
  10. allsnps: YES
  11. ## qpAdm version: 1201
  12. seed: 567625329
  13. read 1073741824 bytes
  14. read 2147483648 bytes
  15. read 3213231878 bytes
  16. packed geno read OK
  17. end of inpack
  18.  
  19. left pops:
  20. Sweden_BattleAxe.SG
  21. Germany_CordedWare
  22. Poland_Globular_Amphora
  23.  
  24. right pops:
  25. Cameroon_SMA.DG
  26. Pinarbasi
  27. MA1
  28. Israel_PPNB
  29. Brazil_LapaDoSanto_9600BP
  30. Kostenki14a
  31. Tianyuan
  32. WSHG1
  33. Iran_GanjDareh_N
  34. Satsurblia_HG
  35. Mongolia_North_N
  36. Russia_HG_Karelia
  37. Serbia_EN_Starcevo
  38.  
  39. 0 Sweden_BattleAxe.SG 1
  40. 1 Germany_CordedWare 10
  41. 2 Poland_Globular_Amphora 5
  42. 3 Cameroon_SMA.DG 1
  43. 4 Pinarbasi 1
  44. 5 MA1 1
  45. 6 Israel_PPNB 1
  46. 7 Brazil_LapaDoSanto_9600BP 4
  47. 8 Kostenki14a 1
  48. 9 Tianyuan 1
  49. 10 WSHG1 1
  50. 11 Iran_GanjDareh_N 8
  51. 12 Satsurblia_HG 1
  52. 13 Mongolia_North_N 5
  53. 14 Russia_HG_Karelia 2
  54. 15 Serbia_EN_Starcevo 1
  55. jackknife block size: 0.050
  56. snps: 1150121 indivs: 44
  57. number of blocks for block jackknife: 714
  58. ## ncols: 1150121
  59. coverage: Sweden_BattleAxe.SG 598273
  60. coverage: Germany_CordedWare 1108998
  61. coverage: Poland_Globular_Amphora 748500
  62. coverage: Cameroon_SMA.DG 1140138
  63. coverage: Pinarbasi 848431
  64. coverage: MA1 805960
  65. coverage: Israel_PPNB 737560
  66. coverage: Brazil_LapaDoSanto_9600BP 883139
  67. coverage: Kostenki14a 1068326
  68. coverage: Tianyuan 885079
  69. coverage: WSHG1 805417
  70. coverage: Iran_GanjDareh_N 1057358
  71. coverage: Satsurblia_HG 801311
  72. coverage: Mongolia_North_N 1057834
  73. coverage: Russia_HG_Karelia 1010733
  74. coverage: Serbia_EN_Starcevo 816289
  75. Effective number of blocks: 621.315
  76. numsnps used: 1150121
  77. codimension 1
  78. f4info:
  79. f4rank: 1 dof: 11 chisq: 30.943 tail: 0.00112473323 dofdiff: 13 chisqdiff: -30.943 taildiff: 1
  80. B:
  81. scale 1.000
  82. Pinarbasi -1.062
  83. MA1 1.075
  84. Israel_PPNB -1.290
  85. Brazil_LapaDoSanto_9600BP 1.090
  86. Kostenki14a 0.086
  87. Tianyuan 0.335
  88. WSHG1 1.815
  89. Iran_GanjDareh_N 0.562
  90. Satsurblia_HG 0.440
  91. Mongolia_North_N 0.549
  92. Russia_HG_Karelia 1.280
  93. Serbia_EN_Starcevo -1.002
  94. A:
  95. scale 910.887
  96. Germany_CordedWare 0.514
  97. Poland_Globular_Amphora -1.318
  98.  
  99.  
  100. full rank
  101. f4info:
  102. f4rank: 2 dof: 0 chisq: 0.000 tail: 1 dofdiff: 11 chisqdiff: 30.943 taildiff: 0.00112473323
  103. B:
  104. scale 849.443 698.783
  105. Pinarbasi 0.408 1.665
  106. MA1 0.985 -0.784
  107. Israel_PPNB 0.165 1.818
  108. Brazil_LapaDoSanto_9600BP 1.508 -0.442
  109. Kostenki14a 0.408 0.161
  110. Tianyuan 1.045 0.277
  111. WSHG1 1.531 -1.305
  112. Iran_GanjDareh_N 1.170 0.061
  113. Satsurblia_HG 0.780 -0.088
  114. Mongolia_North_N 0.747 -0.234
  115. Russia_HG_Karelia 1.469 -0.680
  116. Serbia_EN_Starcevo 0.514 1.667
  117. A:
  118. scale 1.414 1.414
  119. Germany_CordedWare 1.414 0.000
  120. Poland_Globular_Amphora 0.000 1.414
  121.  
  122.  
  123. best coefficients: 0.720 0.280
  124. Jackknife mean: 0.719346879 0.280653121
  125. std. errors: 0.057 0.057
  126.  
  127. error covariance (* 1,000,000)
  128. 3229 -3229
  129. -3229 3229
  130.  
  131.  
  132. summ: Sweden_BattleAxe.SG 2 0.001125 0.719 0.281 3229 -3229 3229
  133.  
  134. fixed pat wt dof chisq tail prob
  135. 00 0 11 30.943 0.00112473 0.720 0.280
  136. 01 1 12 55.421 1.52073e-07 1.000 0.000
  137. 10 1 12 193.886 0 0.000 1.000
  138. best pat: 00 0.00112473 - -
  139. best pat: 01 1.52073e-07 chi(nested): 24.478 p-value for nested model: 7.51457e-07
  140.  
  141. coeffs: 0.720 0.280
  142.  
  143. ## dscore:: f_4(Base, Fit, Rbase, right2)
  144. ## genstat:: f_4(Base, Fit, right1, right2)
  145.  
  146. details: Germany_CordedWare Pinarbasi 0.000480 1.334578
  147. details: Poland_Globular_Amphora Pinarbasi 0.002382 6.705756
  148. dscore: Pinarbasi f4: 0.001014 Z: 3.020875
  149.  
  150. details: Germany_CordedWare MA1 0.001160 3.296028
  151. details: Poland_Globular_Amphora MA1 -0.001122 -3.272970
  152. dscore: MA1 f4: 0.000520 Z: 1.586238
  153.  
  154. details: Germany_CordedWare Israel_PPNB 0.000194 0.521095
  155. details: Poland_Globular_Amphora Israel_PPNB 0.002601 7.094716
  156. dscore: Israel_PPNB f4: 0.000869 Z: 2.501564
  157.  
  158. details: Germany_CordedWare Brazil_LapaDoSanto_9600BP 0.001776 5.302439
  159. details: Poland_Globular_Amphora Brazil_LapaDoSanto_9600BP -0.000633 -1.891430
  160. dscore: Brazil_LapaDoSanto_9600BP f4: 0.001100 Z: 3.519959
  161.  
  162. details: Germany_CordedWare Kostenki14a 0.000481 1.303135
  163. details: Poland_Globular_Amphora Kostenki14a 0.000230 0.654743
  164. dscore: Kostenki14a f4: 0.000410 Z: 1.196333
  165.  
  166. details: Germany_CordedWare Tianyuan 0.001230 3.490112
  167. details: Poland_Globular_Amphora Tianyuan 0.000397 1.131502
  168. dscore: Tianyuan f4: 0.000997 Z: 3.027512
  169.  
  170. details: Germany_CordedWare WSHG1 0.001803 4.332995
  171. details: Poland_Globular_Amphora WSHG1 -0.001868 -4.338333
  172. dscore: WSHG1 f4: 0.000773 Z: 1.940914
  173.  
  174. details: Germany_CordedWare Iran_GanjDareh_N 0.001377 4.878868
  175. details: Poland_Globular_Amphora Iran_GanjDareh_N 0.000088 0.316640
  176. dscore: Iran_GanjDareh_N f4: 0.001016 Z: 3.863185
  177.  
  178. details: Germany_CordedWare Satsurblia_HG 0.000918 2.872237
  179. details: Poland_Globular_Amphora Satsurblia_HG -0.000126 -0.415867
  180. dscore: Satsurblia_HG f4: 0.000625 Z: 2.123291
  181.  
  182. details: Germany_CordedWare Mongolia_North_N 0.000879 2.896772
  183. details: Poland_Globular_Amphora Mongolia_North_N -0.000334 -1.144766
  184. dscore: Mongolia_North_N f4: 0.000539 Z: 1.916183
  185.  
  186. details: Germany_CordedWare Russia_HG_Karelia 0.001730 4.638692
  187. details: Poland_Globular_Amphora Russia_HG_Karelia -0.000973 -2.716872
  188. dscore: Russia_HG_Karelia f4: 0.000972 Z: 2.797647
  189.  
  190. details: Germany_CordedWare Serbia_EN_Starcevo 0.000605 1.677675
  191. details: Poland_Globular_Amphora Serbia_EN_Starcevo 0.002386 6.686555
  192. dscore: Serbia_EN_Starcevo f4: 0.001105 Z: 3.290125
  193.  
  194. gendstat: Cameroon_SMA.DG Pinarbasi 3.021
  195. gendstat: Cameroon_SMA.DG MA1 1.586
  196. gendstat: Cameroon_SMA.DG Israel_PPNB 2.502
  197. gendstat: Cameroon_SMA.DG Brazil_LapaDoSanto_9600BP 3.520
  198. gendstat: Cameroon_SMA.DG Kostenki14a 1.196
  199. gendstat: Cameroon_SMA.DG Tianyuan 3.028
  200. gendstat: Cameroon_SMA.DG WSHG1 1.941
  201. gendstat: Cameroon_SMA.DG Iran_GanjDareh_N 3.863
  202. gendstat: Cameroon_SMA.DG Satsurblia_HG 2.123
  203. gendstat: Cameroon_SMA.DG Mongolia_North_N 1.916
  204. gendstat: Cameroon_SMA.DG Russia_HG_Karelia 2.798
  205. gendstat: Cameroon_SMA.DG Serbia_EN_Starcevo 3.290
  206. gendstat: Pinarbasi MA1 -1.245
  207. gendstat: Pinarbasi Israel_PPNB -0.386
  208. gendstat: Pinarbasi Brazil_LapaDoSanto_9600BP 0.241
  209. gendstat: Pinarbasi Kostenki14a -1.641
  210. gendstat: Pinarbasi Tianyuan -0.043
  211. gendstat: Pinarbasi WSHG1 -0.562
  212. gendstat: Pinarbasi Iran_GanjDareh_N 0.007
  213. gendstat: Pinarbasi Satsurblia_HG -1.063
  214. gendstat: Pinarbasi Mongolia_North_N -1.439
  215. gendstat: Pinarbasi Russia_HG_Karelia -0.106
  216. gendstat: Pinarbasi Serbia_EN_Starcevo 0.248
  217. gendstat: MA1 Israel_PPNB 0.877
  218. gendstat: MA1 Brazil_LapaDoSanto_9600BP 1.774
  219. gendstat: MA1 Kostenki14a -0.290
  220. gendstat: MA1 Tianyuan 1.257
  221. gendstat: MA1 WSHG1 0.674
  222. gendstat: MA1 Iran_GanjDareh_N 1.534
  223. gendstat: MA1 Satsurblia_HG 0.283
  224. gendstat: MA1 Mongolia_North_N 0.060
  225. gendstat: MA1 Russia_HG_Karelia 1.246
  226. gendstat: MA1 Serbia_EN_Starcevo 1.453
  227. gendstat: Israel_PPNB Brazil_LapaDoSanto_9600BP 0.621
  228. gendstat: Israel_PPNB Kostenki14a -1.171
  229. gendstat: Israel_PPNB Tianyuan 0.319
  230. gendstat: Israel_PPNB WSHG1 -0.216
  231. gendstat: Israel_PPNB Iran_GanjDareh_N 0.442
  232. gendstat: Israel_PPNB Satsurblia_HG -0.640
  233. gendstat: Israel_PPNB Mongolia_North_N -0.951
  234. gendstat: Israel_PPNB Russia_HG_Karelia 0.253
  235. gendstat: Israel_PPNB Serbia_EN_Starcevo 0.646
  236. gendstat: Brazil_LapaDoSanto_9600BP Kostenki14a -2.067
  237. gendstat: Brazil_LapaDoSanto_9600BP Tianyuan -0.307
  238. gendstat: Brazil_LapaDoSanto_9600BP WSHG1 -0.946
  239. gendstat: Brazil_LapaDoSanto_9600BP Iran_GanjDareh_N -0.315
  240. gendstat: Brazil_LapaDoSanto_9600BP Satsurblia_HG -1.376
  241. gendstat: Brazil_LapaDoSanto_9600BP Mongolia_North_N -2.347
  242. gendstat: Brazil_LapaDoSanto_9600BP Russia_HG_Karelia -0.409
  243. gendstat: Brazil_LapaDoSanto_9600BP Serbia_EN_Starcevo 0.012
  244. gendstat: Kostenki14a Tianyuan 1.634
  245. gendstat: Kostenki14a WSHG1 0.932
  246. gendstat: Kostenki14a Iran_GanjDareh_N 1.982
  247. gendstat: Kostenki14a Satsurblia_HG 0.578
  248. gendstat: Kostenki14a Mongolia_North_N 0.419
  249. gendstat: Kostenki14a Russia_HG_Karelia 1.610
  250. gendstat: Kostenki14a Serbia_EN_Starcevo 1.803
  251. gendstat: Tianyuan WSHG1 -0.547
  252. gendstat: Tianyuan Iran_GanjDareh_N 0.062
  253. gendstat: Tianyuan Satsurblia_HG -0.998
  254. gendstat: Tianyuan Mongolia_North_N -1.566
  255. gendstat: Tianyuan Russia_HG_Karelia -0.063
  256. gendstat: Tianyuan Serbia_EN_Starcevo 0.277
  257. gendstat: WSHG1 Iran_GanjDareh_N 0.694
  258. gendstat: WSHG1 Satsurblia_HG -0.364
  259. gendstat: WSHG1 Mongolia_North_N -0.665
  260. gendstat: WSHG1 Russia_HG_Karelia 0.560
  261. gendstat: WSHG1 Serbia_EN_Starcevo 0.755
  262. gendstat: Iran_GanjDareh_N Satsurblia_HG -1.361
  263. gendstat: Iran_GanjDareh_N Mongolia_North_N -1.993
  264. gendstat: Iran_GanjDareh_N Russia_HG_Karelia -0.139
  265. gendstat: Iran_GanjDareh_N Serbia_EN_Starcevo 0.284
  266. gendstat: Satsurblia_HG Mongolia_North_N -0.275
  267. gendstat: Satsurblia_HG Russia_HG_Karelia 0.909
  268. gendstat: Satsurblia_HG Serbia_EN_Starcevo 1.316
  269. gendstat: Mongolia_North_N Russia_HG_Karelia 1.384
  270. gendstat: Mongolia_North_N Serbia_EN_Starcevo 1.730
  271. gendstat: Russia_HG_Karelia Serbia_EN_Starcevo 0.327
  272.  
  273. ##end of qpAdm: 256.238 seconds cpu 1350.291 Mbytes in use
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