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misnomer001
Aug 17th, 2022
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  1. qpAdm: parameter file: parqpadm
  2. ### THE INPUT PARAMETERS
  3. ##PARAMETER NAME: VALUE
  4. popleft: left
  5. popright: right
  6. details: YES
  7. allsnps: YES
  8. inbreed: NO
  9. oldallsnps: NO
  10. S1: newpush1
  11. S1X: newpush1
  12. indivname: newpush1.ind
  13. snpname: newpush1.snp
  14. genotypename: newpush1.geno
  15. ## qpAdm version: 1520
  16. seed: 639354319
  17. inbreed set NO
  18. inbreed set NO
  19. tmp: /tmp/fsx.32733
  20.  
  21. left pops:
  22. Ror
  23. Tajikistan_C_Sarazm
  24. Russia_MLBA_Sintashta
  25. Irula.DG
  26. CHG_Kotias
  27. Tarim_EMBA1
  28.  
  29. right pops:
  30. Mbuti.DG
  31. CHG_Satsurblia
  32. EHG
  33. China_YR_MN
  34. Turkey_Boncuklu_N
  35. Russia_Shamanka_Eneolithic.SG
  36. WSHG
  37. PPN
  38. Serbia_IronGates_Mesolithic
  39. Iran_GanjDareh_N
  40. Turkey_N
  41. ONG.SG
  42. IVCp
  43.  
  44. codimension 1
  45. f4info:
  46. f4rank: 4 dof: 8 chisq: 11.899 tail: 0.155783257 dofdiff: 10 chisqdiff: -11.899 taildiff: 1
  47. B:
  48. scale 1.000 1.000 1.000 1.000
  49. CHG_Satsurblia -0.194 1.712 -1.703 0.701
  50. EHG 1.978 0.408 0.289 0.451
  51. China_YR_MN 0.528 -0.920 -0.257 0.501
  52. Turkey_Boncuklu_N 0.125 1.228 1.069 0.364
  53. Russia_Shamanka_Eneolithic.SG 0.811 -0.870 -0.463 0.602
  54. WSHG 2.537 -0.119 -0.839 -0.631
  55. PPN 0.086 1.106 0.982 0.052
  56. Serbia_IronGates_Mesolithic 0.759 1.101 1.867 1.374
  57. Iran_GanjDareh_N 0.004 0.885 -0.899 -2.450
  58. Turkey_N 0.078 1.281 1.173 0.165
  59. ONG.SG 0.187 -0.958 -0.095 0.555
  60. IVCp 0.195 0.011 -0.501 -1.390
  61. A:
  62. scale 90.189 117.180 194.365 423.312
  63. Tajikistan_C_Sarazm 0.068 0.534 -0.499 -1.644
  64. Russia_MLBA_Sintashta 0.537 0.945 0.801 0.270
  65. Irula.DG -0.597 -1.313 -0.238 0.313
  66. CHG_Kotias -0.416 1.399 -1.847 1.423
  67. Tarim_EMBA1 2.044 -0.377 -0.801 0.320
  68.  
  69.  
  70. full rank
  71. f4info:
  72. f4rank: 5 dof: 0 chisq: 0.000 tail: 1 dofdiff: 8 chisqdiff: 11.899 taildiff: 0.155783257
  73. B:
  74. scale 149.283 84.725 73.224 73.549 42.197
  75. CHG_Satsurblia 1.371 0.545 -1.147 3.052 -0.097
  76. EHG -0.013 1.388 -1.378 -0.409 1.794
  77. China_YR_MN -0.829 -0.418 0.527 -0.685 0.711
  78. Turkey_Boncuklu_N 0.131 1.298 -1.205 0.358 -0.228
  79. Russia_Shamanka_Eneolithic.SG -0.780 -0.326 0.339 -0.594 1.007
  80. WSHG 0.919 0.914 -1.064 -0.489 2.603
  81. PPN 0.293 1.154 -1.076 0.255 -0.232
  82. Serbia_IronGates_Mesolithic -0.662 1.878 -1.375 -0.218 0.311
  83. Iran_GanjDareh_N 2.336 0.162 -0.821 0.790 -0.035
  84. Turkey_N 0.236 1.330 -1.248 0.322 -0.299
  85. ONG.SG -0.957 -0.551 0.712 -0.700 0.357
  86. IVCp 1.005 -0.122 -0.155 -0.021 0.237
  87. A:
  88. scale 2.236 2.236 2.236 2.236 2.236
  89. Tajikistan_C_Sarazm 2.236 0.000 0.000 0.000 0.000
  90. Russia_MLBA_Sintashta 0.000 2.236 0.000 0.000 0.000
  91. Irula.DG 0.000 0.000 2.236 0.000 0.000
  92. CHG_Kotias 0.000 0.000 0.000 2.236 0.000
  93. Tarim_EMBA1 0.000 0.000 0.000 0.000 2.236
  94.  
  95.  
  96. best coefficients: 0.181 0.364 0.384 0.051 0.021
  97. totmean: 0.181 0.364 0.384 0.051 0.021
  98. boot mean: 0.181 0.364 0.384 0.051 0.021
  99. std. errors: 0.021 0.011 0.010 0.016 0.008
  100.  
  101. error covariance (* 1,000,000)
  102. 435 -20 -96 -254 -65
  103. -20 112 3 -65 -31
  104. -96 3 106 2 -16
  105. -254 -65 2 261 56
  106. -65 -31 -16 56 57
  107.  
  108.  
  109. summ: Ror 5 0.155783 0.181 0.364 0.384 0.051 0.021 435 -20 -96 -254 -65 ...
  110. 112 3 -65 -31 106 ...
  111. 2 -16 261 56 57
  112.  
  113. fixed pat wt dof chisq tail prob
  114. 00000 0 8 11.899 0.155783 0.181 0.364 0.384 0.051 0.021
  115. 00001 1 9 330.336 0 0.317 0.375 0.377 -0.069 0.000 infeasible
  116. 00010 1 9 25.750 0.00224449 0.231 0.375 0.384 0.000 0.010
  117. 00100 1 9 326.638 0 16.143 2.860 0.000 -15.065 -2.938 infeasible
  118. 01000 1 9 331.499 0 -2.095 0.000 0.435 2.210 0.450 infeasible
  119. 10000 1 9 90.221 1.47013e-15 0.000 0.365 0.419 0.167 0.048
  120. 00011 2 10 26.070 0.00364664 0.232 0.379 0.389 0.000 0.000
  121. 00101 2 10 406.296 0 3.025 0.495 0.000 -2.520 0.000 infeasible
  122. 00110 2 10 700.435 0 0.855 0.116 0.000 0.000 0.029
  123. 01001 2 10 434.931 0 -6.579 0.000 1.251 6.328 0.000 infeasible
  124. 01010 2 10 600.727 0 0.703 0.000 0.274 0.000 0.023
  125. 01100 2 10 335.962 0 -58.372 0.000 0.000 49.637 9.736 infeasible
  126. 10001 2 10 124.754 5.47187e-22 0.000 0.402 0.456 0.142 0.000
  127. 10010 2 10 247.420 0 0.000 0.469 0.517 0.000 0.015
  128. 10100 2 10 696.388 0 0.000 -0.106 0.000 0.905 0.201 infeasible
  129. 11000 2 10 486.895 0 0.000 0.000 0.307 0.563 0.130
  130. 00111 3 11 705.446 0 0.883 0.117 0.000 0.000 0.000
  131. 01011 3 11 602.778 0 0.719 0.000 0.281 0.000 0.000
  132. 01101 3 11 394.122 0 3.459 0.000 0.000 -2.459 0.000 infeasible
  133. 01110 3 11 731.798 0 0.969 0.000 0.000 0.000 0.031
  134. 10011 3 11 250.177 0 0.000 0.477 0.523 0.000 0.000
  135. 10101 3 11 846.516 0 0.000 -0.166 0.000 1.166 0.000 infeasible
  136. 10110 3 11 3597.156 0 0.000 0.687 0.000 0.000 0.313
  137. 11001 3 11 618.916 0 0.000 0.000 0.358 0.642 0.000
  138. 11010 3 11 1444.915 0 0.000 0.000 0.941 0.000 0.059
  139. 11100 3 11 707.732 0 0.000 0.000 0.000 0.805 0.195
  140. 01111 4 12 725.712 0 1.000 0.000 0.000 0.000 0.000
  141. 10111 4 12 3980.037 0 0.000 1.000 0.000 0.000 0.000
  142. 11011 4 12 1460.448 0 0.000 0.000 1.000 0.000 0.000
  143. 11101 4 12 853.105 0 0.000 0.000 0.000 1.000 0.000
  144. 11110 4 12 5243.621 0 0.000 0.000 0.000 0.000 1.000
  145. best pat: 00000 0.155783 - -
  146. best pat: 10000 1.47013e-15 chi(nested): 78.322 p-value for nested model: 8.75329e-19
  147. best pat: 10001 5.47187e-22 chi(nested): 34.533 p-value for nested model: 4.18995e-09
  148. best pat: 10011 2.56485e-47 chi(nested): 125.423 p-value for nested model: 4.11205e-29
  149. best pat: 01111 1.37792e-147 not nested
  150.  
  151. coeffs: 0.181 0.364 0.384 0.051 0.021
  152.  
  153. ## dscore:: f_4(Base, Fit, Rbase, right2)
  154. ## genstat:: f_4(Base, Fit, right1, right2)
  155.  
  156. details: Tajikistan_C_Sarazm CHG_Satsurblia 0.009184 6.632046
  157. details: Russia_MLBA_Sintashta CHG_Satsurblia 0.006434 9.211130
  158. details: Irula.DG CHG_Satsurblia -0.015659 -13.276586
  159. details: CHG_Kotias CHG_Satsurblia 0.041491 20.391366
  160. details: Tarim_EMBA1 CHG_Satsurblia -0.002309 -1.888199
  161. dscore: CHG_Satsurblia f4: 0.000050 Z: 0.076524
  162.  
  163. details: Tajikistan_C_Sarazm EHG -0.000084 -0.073023
  164. details: Russia_MLBA_Sintashta EHG 0.016382 27.507656
  165. details: Irula.DG EHG -0.018814 -19.995698
  166. details: CHG_Kotias EHG -0.005557 -3.739935
  167. details: Tarim_EMBA1 EHG 0.042524 34.510625
  168. dscore: EHG f4: -0.000670 Z: -1.232751
  169.  
  170. details: Tajikistan_C_Sarazm China_YR_MN -0.005555 -5.039996
  171. details: Russia_MLBA_Sintashta China_YR_MN -0.004935 -8.547195
  172. details: Irula.DG China_YR_MN 0.007198 7.771513
  173. details: CHG_Kotias China_YR_MN -0.009314 -6.999966
  174. details: Tarim_EMBA1 China_YR_MN 0.016850 16.828158
  175. dscore: China_YR_MN f4: -0.000163 Z: -0.312950
  176.  
  177. details: Tajikistan_C_Sarazm Turkey_Boncuklu_N 0.000875 0.861223
  178. details: Russia_MLBA_Sintashta Turkey_Boncuklu_N 0.015322 28.917947
  179. details: Irula.DG Turkey_Boncuklu_N -0.016451 -18.557797
  180. details: CHG_Kotias Turkey_Boncuklu_N 0.004864 3.904165
  181. details: Tarim_EMBA1 Turkey_Boncuklu_N -0.005414 -5.853227
  182. dscore: Turkey_Boncuklu_N f4: -0.000439 Z: -0.904483
  183.  
  184. details: Tajikistan_C_Sarazm Russia_Shamanka_Eneolithic.SG -0.005228 -5.147712
  185. details: Russia_MLBA_Sintashta Russia_Shamanka_Eneolithic.SG -0.003851 -7.294809
  186. details: Irula.DG Russia_Shamanka_Eneolithic.SG 0.004627 5.479048
  187. details: CHG_Kotias Russia_Shamanka_Eneolithic.SG -0.008080 -6.765998
  188. details: Tarim_EMBA1 Russia_Shamanka_Eneolithic.SG 0.023868 25.105599
  189. dscore: Russia_Shamanka_Eneolithic.SG f4: -0.000488 Z: -1.050242
  190.  
  191. details: Tajikistan_C_Sarazm WSHG 0.006157 4.953527
  192. details: Russia_MLBA_Sintashta WSHG 0.010787 17.188407
  193. details: Irula.DG WSHG -0.014532 -14.024365
  194. details: CHG_Kotias WSHG -0.006648 -4.621912
  195. details: Tarim_EMBA1 WSHG 0.061675 50.110580
  196. dscore: WSHG f4: 0.000404 Z: 0.678686
  197.  
  198. details: Tajikistan_C_Sarazm PPN 0.001965 1.796730
  199. details: Russia_MLBA_Sintashta PPN 0.013620 22.547134
  200. details: Irula.DG PPN -0.014700 -15.489930
  201. details: CHG_Kotias PPN 0.003465 2.566227
  202. details: Tarim_EMBA1 PPN -0.005502 -5.249556
  203. dscore: PPN f4: -0.000263 Z: -0.464450
  204.  
  205. details: Tajikistan_C_Sarazm Serbia_IronGates_Mesolithic -0.004437 -4.735611
  206. details: Russia_MLBA_Sintashta Serbia_IronGates_Mesolithic 0.022171 42.707122
  207. details: Irula.DG Serbia_IronGates_Mesolithic -0.018772 -21.764837
  208. details: CHG_Kotias Serbia_IronGates_Mesolithic -0.002965 -2.376033
  209. details: Tarim_EMBA1 Serbia_IronGates_Mesolithic 0.007380 7.574717
  210. dscore: Serbia_IronGates_Mesolithic f4: 0.000073 Z: 0.157162
  211.  
  212. details: Tajikistan_C_Sarazm Iran_GanjDareh_N 0.015645 15.849199
  213. details: Russia_MLBA_Sintashta Iran_GanjDareh_N 0.001912 3.822518
  214. details: Irula.DG Iran_GanjDareh_N -0.011212 -13.312779
  215. details: CHG_Kotias Iran_GanjDareh_N 0.010737 9.134250
  216. details: Tarim_EMBA1 Iran_GanjDareh_N -0.000823 -0.881941
  217. dscore: Iran_GanjDareh_N f4: -0.000252 Z: -0.531516
  218.  
  219. details: Tajikistan_C_Sarazm Turkey_N 0.001581 1.850355
  220. details: Russia_MLBA_Sintashta Turkey_N 0.015701 33.317765
  221. details: Irula.DG Turkey_N -0.017045 -21.353675
  222. details: CHG_Kotias Turkey_N 0.004383 3.944792
  223. details: Tarim_EMBA1 Turkey_N -0.007086 -8.318118
  224. dscore: Turkey_N f4: -0.000460 Z: -1.062334
  225.  
  226. details: Tajikistan_C_Sarazm ONG.SG -0.006411 -5.914347
  227. details: Russia_MLBA_Sintashta ONG.SG -0.006508 -12.116177
  228. details: Irula.DG ONG.SG 0.009729 10.802204
  229. details: CHG_Kotias ONG.SG -0.009522 -7.646237
  230. details: Tarim_EMBA1 ONG.SG 0.008471 8.922060
  231. dscore: ONG.SG f4: -0.000103 Z: -0.207563
  232.  
  233. details: Tajikistan_C_Sarazm IVCp 0.006732 7.378824
  234. details: Russia_MLBA_Sintashta IVCp -0.001436 -2.945594
  235. details: Irula.DG IVCp -0.002120 -2.610028
  236. details: CHG_Kotias IVCp -0.000284 -0.253713
  237. details: Tarim_EMBA1 IVCp 0.005626 6.709995
  238. dscore: IVCp f4: -0.000018 Z: -0.039456
  239.  
  240. gendstat: Mbuti.DG CHG_Satsurblia 0.077
  241. gendstat: Mbuti.DG EHG -1.233
  242. gendstat: Mbuti.DG China_YR_MN -0.313
  243. gendstat: Mbuti.DG Turkey_Boncuklu_N -0.904
  244. gendstat: Mbuti.DG Russia_Shamanka_Eneolithic.SG -1.050
  245. gendstat: Mbuti.DG WSHG 0.679
  246. gendstat: Mbuti.DG PPN -0.464
  247. gendstat: Mbuti.DG Serbia_IronGates_Mesolithic 0.157
  248. gendstat: Mbuti.DG Iran_GanjDareh_N -0.532
  249. gendstat: Mbuti.DG Turkey_N -1.062
  250. gendstat: Mbuti.DG ONG.SG -0.208
  251. gendstat: Mbuti.DG IVCp -0.039
  252. gendstat: CHG_Satsurblia EHG -1.098
  253. gendstat: CHG_Satsurblia China_YR_MN -0.308
  254. gendstat: CHG_Satsurblia Turkey_Boncuklu_N -0.745
  255. gendstat: CHG_Satsurblia Russia_Shamanka_Eneolithic.SG -0.822
  256. gendstat: CHG_Satsurblia WSHG 0.490
  257. gendstat: CHG_Satsurblia PPN -0.450
  258. gendstat: CHG_Satsurblia Serbia_IronGates_Mesolithic 0.037
  259. gendstat: CHG_Satsurblia Iran_GanjDareh_N -0.495
  260. gendstat: CHG_Satsurblia Turkey_N -0.856
  261. gendstat: CHG_Satsurblia ONG.SG -0.231
  262. gendstat: CHG_Satsurblia IVCp -0.113
  263. gendstat: EHG China_YR_MN 0.877
  264. gendstat: EHG Turkey_Boncuklu_N 0.438
  265. gendstat: EHG Russia_Shamanka_Eneolithic.SG 0.361
  266. gendstat: EHG WSHG 2.102
  267. gendstat: EHG PPN 0.687
  268. gendstat: EHG Serbia_IronGates_Mesolithic 1.738
  269. gendstat: EHG Iran_GanjDareh_N 0.810
  270. gendstat: EHG Turkey_N 0.446
  271. gendstat: EHG ONG.SG 1.008
  272. gendstat: EHG IVCp 1.275
  273. gendstat: China_YR_MN Turkey_Boncuklu_N -0.494
  274. gendstat: China_YR_MN Russia_Shamanka_Eneolithic.SG -0.973
  275. gendstat: China_YR_MN WSHG 0.958
  276. gendstat: China_YR_MN PPN -0.163
  277. gendstat: China_YR_MN Serbia_IronGates_Mesolithic 0.478
  278. gendstat: China_YR_MN Iran_GanjDareh_N -0.164
  279. gendstat: China_YR_MN Turkey_N -0.591
  280. gendstat: China_YR_MN ONG.SG 0.127
  281. gendstat: China_YR_MN IVCp 0.303
  282. gendstat: Turkey_Boncuklu_N Russia_Shamanka_Eneolithic.SG -0.098
  283. gendstat: Turkey_Boncuklu_N WSHG 1.422
  284. gendstat: Turkey_Boncuklu_N PPN 0.343
  285. gendstat: Turkey_Boncuklu_N Serbia_IronGates_Mesolithic 1.269
  286. gendstat: Turkey_Boncuklu_N Iran_GanjDareh_N 0.401
  287. gendstat: Turkey_Boncuklu_N Turkey_N -0.066
  288. gendstat: Turkey_Boncuklu_N ONG.SG 0.618
  289. gendstat: Turkey_Boncuklu_N IVCp 0.903
  290. gendstat: Russia_Shamanka_Eneolithic.SG WSHG 1.671
  291. gendstat: Russia_Shamanka_Eneolithic.SG PPN 0.400
  292. gendstat: Russia_Shamanka_Eneolithic.SG Serbia_IronGates_Mesolithic 1.279
  293. gendstat: Russia_Shamanka_Eneolithic.SG Iran_GanjDareh_N 0.482
  294. gendstat: Russia_Shamanka_Eneolithic.SG Turkey_N 0.062
  295. gendstat: Russia_Shamanka_Eneolithic.SG ONG.SG 0.908
  296. gendstat: Russia_Shamanka_Eneolithic.SG IVCp 1.077
  297. gendstat: WSHG PPN -1.015
  298. gendstat: WSHG Serbia_IronGates_Mesolithic -0.656
  299. gendstat: WSHG Iran_GanjDareh_N -1.172
  300. gendstat: WSHG Turkey_N -1.581
  301. gendstat: WSHG ONG.SG -0.838
  302. gendstat: WSHG IVCp -0.777
  303. gendstat: PPN Serbia_IronGates_Mesolithic 0.649
  304. gendstat: PPN Iran_GanjDareh_N 0.020
  305. gendstat: PPN Turkey_N -0.429
  306. gendstat: PPN ONG.SG 0.263
  307. gendstat: PPN IVCp 0.449
  308. gendstat: Serbia_IronGates_Mesolithic Iran_GanjDareh_N -0.730
  309. gendstat: Serbia_IronGates_Mesolithic Turkey_N -1.561
  310. gendstat: Serbia_IronGates_Mesolithic ONG.SG -0.360
  311. gendstat: Serbia_IronGates_Mesolithic IVCp -0.208
  312. gendstat: Iran_GanjDareh_N Turkey_N -0.529
  313. gendstat: Iran_GanjDareh_N ONG.SG 0.285
  314. gendstat: Iran_GanjDareh_N IVCp 0.554
  315. gendstat: Turkey_N ONG.SG 0.735
  316. gendstat: Turkey_N IVCp 1.124
  317. gendstat: ONG.SG IVCp 0.179
  318.  
  319. removing /tmp/fsx.32733
  320. ##end of qpAdm: 51.841 seconds cpu 1.712 Mbytes in use
  321.  
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