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RG701
Jul 16th, 2022
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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/robertDataset2.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: 1608853304
  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. Yam_Samara
  21. Russia_Steppe_Eneolithic
  22. Russia_Khvalynsk_Eneolithic
  23. Russia_Caucasus_Maikop
  24.  
  25. right pops:
  26. Cameroon_SMA.DG
  27. Morocco_Iberomaurusian
  28. MA1
  29. Brazil_LapaDoSanto_9600BP
  30. Kostenki14a
  31. Tianyuan
  32. Iran_GanjDareh_N
  33. Satsurblia_HG
  34. Pinarbasi
  35. WSHG1
  36. Tagliente_LPaleolithic
  37. Mongolia_North_N
  38. Serbia_EN_Starcevo
  39. Russia_HG_Karelia
  40.  
  41. 0 Yam_Samara 6
  42. 1 Russia_Steppe_Eneolithic 2
  43. 2 Russia_Khvalynsk_Eneolithic 3
  44. 3 Russia_Caucasus_Maikop 2
  45. 4 Cameroon_SMA.DG 1
  46. 5 Morocco_Iberomaurusian 6
  47. 6 MA1 1
  48. 7 Brazil_LapaDoSanto_9600BP 4
  49. 8 Kostenki14a 1
  50. 9 Tianyuan 1
  51. 10 Iran_GanjDareh_N 8
  52. 11 Satsurblia_HG 1
  53. 12 Pinarbasi 1
  54. 13 WSHG1 1
  55. 14 Tagliente_LPaleolithic 1
  56. 15 Mongolia_North_N 5
  57. 16 Serbia_EN_Starcevo 1
  58. 17 Russia_HG_Karelia 2
  59. jackknife block size: 0.050
  60. snps: 1150131 indivs: 47
  61. number of blocks for block jackknife: 714
  62. ## ncols: 1150131
  63. coverage: Yam_Samara 1027282
  64. coverage: Russia_Steppe_Eneolithic 952133
  65. coverage: Russia_Khvalynsk_Eneolithic 758497
  66. coverage: Russia_Caucasus_Maikop 404864
  67. coverage: Cameroon_SMA.DG 1140138
  68. coverage: Morocco_Iberomaurusian 1101342
  69. coverage: MA1 805960
  70. coverage: Brazil_LapaDoSanto_9600BP 883139
  71. coverage: Kostenki14a 1068326
  72. coverage: Tianyuan 885079
  73. coverage: Iran_GanjDareh_N 1057358
  74. coverage: Satsurblia_HG 801311
  75. coverage: Pinarbasi 848431
  76. coverage: WSHG1 805417
  77. coverage: Tagliente_LPaleolithic 186096
  78. coverage: Mongolia_North_N 1057834
  79. coverage: Serbia_EN_Starcevo 816289
  80. coverage: Russia_HG_Karelia 1010733
  81. Effective number of blocks: 616.889
  82. numsnps used: 1150131
  83. codimension 1
  84. f4info:
  85. f4rank: 2 dof: 11 chisq: 14.067 tail: 0.229307368 dofdiff: 13 chisqdiff: -14.067 taildiff: 1
  86. B:
  87. scale 1.000 1.000
  88. Morocco_Iberomaurusian -0.010 -0.923
  89. MA1 1.208 0.631
  90. Brazil_LapaDoSanto_9600BP 0.976 0.181
  91. Kostenki14a 0.366 1.181
  92. Tianyuan 0.471 0.032
  93. Iran_GanjDareh_N -0.304 1.456
  94. Satsurblia_HG -0.353 1.679
  95. Pinarbasi -0.485 -1.373
  96. WSHG1 2.119 0.101
  97. Tagliente_LPaleolithic 0.313 -0.086
  98. Mongolia_North_N 0.436 -0.070
  99. Serbia_EN_Starcevo -0.639 -1.079
  100. Russia_HG_Karelia 2.144 -1.520
  101. A:
  102. scale 718.188 3275.726
  103. Russia_Steppe_Eneolithic 0.131 1.557
  104. Russia_Khvalynsk_Eneolithic 1.277 -0.568
  105. Russia_Caucasus_Maikop -1.163 -0.504
  106.  
  107.  
  108. full rank
  109. f4info:
  110. f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 11 chisqdiff: 14.067 taildiff: 0.229307368
  111. B:
  112. scale 2081.235 549.611 604.348
  113. Morocco_Iberomaurusian -1.082 0.086 0.039
  114. MA1 1.032 1.163 -1.277
  115. Brazil_LapaDoSanto_9600BP -0.122 0.792 -1.170
  116. Kostenki14a 1.131 0.202 -0.523
  117. Tianyuan 0.263 0.500 -0.490
  118. Iran_GanjDareh_N 1.562 -0.314 0.225
  119. Satsurblia_HG 1.409 -0.504 0.128
  120. Pinarbasi -1.617 -0.342 0.490
  121. WSHG1 0.629 2.014 -2.191
  122. Tagliente_LPaleolithic -0.386 0.185 -0.499
  123. Mongolia_North_N -0.162 0.389 -0.534
  124. Serbia_EN_Starcevo -1.328 -0.476 0.725
  125. Russia_HG_Karelia -0.172 2.405 -1.821
  126. A:
  127. scale 1.732 1.732 1.732
  128. Russia_Steppe_Eneolithic 1.732 0.000 0.000
  129. Russia_Khvalynsk_Eneolithic 0.000 1.732 0.000
  130. Russia_Caucasus_Maikop 0.000 0.000 1.732
  131.  
  132.  
  133. best coefficients: 0.255 0.341 0.404
  134. Jackknife mean: 0.253473202 0.342064356 0.404462442
  135. std. errors: 0.095 0.050 0.053
  136.  
  137. error covariance (* 1,000,000)
  138. 9042 -4373 -4669
  139. -4373 2528 1845
  140. -4669 1845 2824
  141.  
  142.  
  143. summ: Yam_Samara 3 0.229307 0.253 0.342 0.404 9042 -4373 -4669 2528 1845 ...
  144. 2824
  145.  
  146. fixed pat wt dof chisq tail prob
  147. 000 0 11 14.067 0.229307 0.255 0.341 0.404
  148. 001 1 12 46.407 5.90031e-06 0.959 0.041 0.000
  149. 010 1 12 44.127 1.45272e-05 0.893 0.000 0.107
  150. 100 1 12 23.034 0.0274359 0.000 0.464 0.536
  151. 011 2 13 46.872 1.01535e-05 1.000 0.000 0.000
  152. 101 2 13 363.140 0 0.000 1.000 0.000
  153. 110 2 13 344.139 0 0.000 0.000 1.000
  154. best pat: 000 0.229307 - -
  155. best pat: 100 0.0274359 chi(nested): 8.967 p-value for nested model: 0.00274852
  156. best pat: 011 1.01535e-05 not nested
  157.  
  158. coeffs: 0.255 0.341 0.404
  159.  
  160. ## dscore:: f_4(Base, Fit, Rbase, right2)
  161. ## genstat:: f_4(Base, Fit, right1, right2)
  162.  
  163. details: Russia_Steppe_Eneolithic Morocco_Iberomaurusian -0.000520 -1.799387
  164. details: Russia_Khvalynsk_Eneolithic Morocco_Iberomaurusian 0.000156 0.623036
  165. details: Russia_Caucasus_Maikop Morocco_Iberomaurusian 0.000064 0.261869
  166. dscore: Morocco_Iberomaurusian f4: -0.000053 Z: -0.297371
  167.  
  168. details: Russia_Steppe_Eneolithic MA1 0.000496 1.446535
  169. details: Russia_Khvalynsk_Eneolithic MA1 0.002115 6.667175
  170. details: Russia_Caucasus_Maikop MA1 -0.002114 -7.047877
  171. dscore: MA1 f4: -0.000005 Z: -0.021570
  172.  
  173. details: Russia_Steppe_Eneolithic Brazil_LapaDoSanto_9600BP -0.000059 -0.171581
  174. details: Russia_Khvalynsk_Eneolithic Brazil_LapaDoSanto_9600BP 0.001441 4.728985
  175. details: Russia_Caucasus_Maikop Brazil_LapaDoSanto_9600BP -0.001936 -6.414359
  176. dscore: Brazil_LapaDoSanto_9600BP f4: -0.000304 Z: -1.354634
  177.  
  178. details: Russia_Steppe_Eneolithic Kostenki14a 0.000543 1.538243
  179. details: Russia_Khvalynsk_Eneolithic Kostenki14a 0.000368 1.139065
  180. details: Russia_Caucasus_Maikop Kostenki14a -0.000866 -3.008577
  181. dscore: Kostenki14a f4: -0.000085 Z: -0.383733
  182.  
  183. details: Russia_Steppe_Eneolithic Tianyuan 0.000126 0.351596
  184. details: Russia_Khvalynsk_Eneolithic Tianyuan 0.000910 2.951390
  185. details: Russia_Caucasus_Maikop Tianyuan -0.000811 -2.573012
  186. dscore: Tianyuan f4: 0.000015 Z: 0.068722
  187.  
  188. details: Russia_Steppe_Eneolithic Iran_GanjDareh_N 0.000750 2.649129
  189. details: Russia_Khvalynsk_Eneolithic Iran_GanjDareh_N -0.000571 -2.134641
  190. details: Russia_Caucasus_Maikop Iran_GanjDareh_N 0.000373 1.490625
  191. dscore: Iran_GanjDareh_N f4: 0.000147 Z: 0.783422
  192.  
  193. details: Russia_Steppe_Eneolithic Satsurblia_HG 0.000677 2.136314
  194. details: Russia_Khvalynsk_Eneolithic Satsurblia_HG -0.000917 -2.951373
  195. details: Russia_Caucasus_Maikop Satsurblia_HG 0.000212 0.767943
  196. dscore: Satsurblia_HG f4: -0.000055 Z: -0.258977
  197.  
  198. details: Russia_Steppe_Eneolithic Pinarbasi -0.000777 -2.221719
  199. details: Russia_Khvalynsk_Eneolithic Pinarbasi -0.000621 -1.839375
  200. details: Russia_Caucasus_Maikop Pinarbasi 0.000811 2.524822
  201. dscore: Pinarbasi f4: -0.000083 Z: -0.343929
  202.  
  203. details: Russia_Steppe_Eneolithic WSHG1 0.000302 0.807663
  204. details: Russia_Khvalynsk_Eneolithic WSHG1 0.003665 10.499723
  205. details: Russia_Caucasus_Maikop WSHG1 -0.003626 -10.284491
  206. dscore: WSHG1 f4: -0.000136 Z: -0.539578
  207.  
  208. details: Russia_Steppe_Eneolithic Tagliente_LPaleolithic -0.000186 -1.127448
  209. details: Russia_Khvalynsk_Eneolithic Tagliente_LPaleolithic 0.000337 1.877388
  210. details: Russia_Caucasus_Maikop Tagliente_LPaleolithic -0.000826 -3.679498
  211. dscore: Tagliente_LPaleolithic f4: -0.000266 Z: -1.951786
  212.  
  213. details: Russia_Steppe_Eneolithic Mongolia_North_N -0.000078 -0.250786
  214. details: Russia_Khvalynsk_Eneolithic Mongolia_North_N 0.000707 2.535017
  215. details: Russia_Caucasus_Maikop Mongolia_North_N -0.000883 -3.187804
  216. dscore: Mongolia_North_N f4: -0.000135 Z: -0.659190
  217.  
  218. details: Russia_Steppe_Eneolithic Serbia_EN_Starcevo -0.000638 -1.892516
  219. details: Russia_Khvalynsk_Eneolithic Serbia_EN_Starcevo -0.000867 -2.653469
  220. details: Russia_Caucasus_Maikop Serbia_EN_Starcevo 0.001200 3.822063
  221. dscore: Serbia_EN_Starcevo f4: 0.000026 Z: 0.111229
  222.  
  223. details: Russia_Steppe_Eneolithic Russia_HG_Karelia -0.000083 -0.222450
  224. details: Russia_Khvalynsk_Eneolithic Russia_HG_Karelia 0.004375 13.103696
  225. details: Russia_Caucasus_Maikop Russia_HG_Karelia -0.003013 -10.075571
  226. dscore: Russia_HG_Karelia f4: 0.000256 Z: 1.123812
  227.  
  228. gendstat: Cameroon_SMA.DG Morocco_Iberomaurusian -0.297
  229. gendstat: Cameroon_SMA.DG MA1 -0.022
  230. gendstat: Cameroon_SMA.DG Brazil_LapaDoSanto_9600BP -1.355
  231. gendstat: Cameroon_SMA.DG Kostenki14a -0.384
  232. gendstat: Cameroon_SMA.DG Tianyuan 0.069
  233. gendstat: Cameroon_SMA.DG Iran_GanjDareh_N 0.783
  234. gendstat: Cameroon_SMA.DG Satsurblia_HG -0.259
  235. gendstat: Cameroon_SMA.DG Pinarbasi -0.344
  236. gendstat: Cameroon_SMA.DG WSHG1 -0.540
  237. gendstat: Cameroon_SMA.DG Tagliente_LPaleolithic -1.952
  238. gendstat: Cameroon_SMA.DG Mongolia_North_N -0.659
  239. gendstat: Cameroon_SMA.DG Serbia_EN_Starcevo 0.111
  240. gendstat: Cameroon_SMA.DG Russia_HG_Karelia 1.124
  241. gendstat: Morocco_Iberomaurusian MA1 0.208
  242. gendstat: Morocco_Iberomaurusian Brazil_LapaDoSanto_9600BP -1.173
  243. gendstat: Morocco_Iberomaurusian Kostenki14a -0.145
  244. gendstat: Morocco_Iberomaurusian Tianyuan 0.311
  245. gendstat: Morocco_Iberomaurusian Iran_GanjDareh_N 1.051
  246. gendstat: Morocco_Iberomaurusian Satsurblia_HG -0.005
  247. gendstat: Morocco_Iberomaurusian Pinarbasi -0.129
  248. gendstat: Morocco_Iberomaurusian WSHG1 -0.332
  249. gendstat: Morocco_Iberomaurusian Tagliente_LPaleolithic -1.066
  250. gendstat: Morocco_Iberomaurusian Mongolia_North_N -0.417
  251. gendstat: Morocco_Iberomaurusian Serbia_EN_Starcevo 0.351
  252. gendstat: Morocco_Iberomaurusian Russia_HG_Karelia 1.370
  253. gendstat: MA1 Brazil_LapaDoSanto_9600BP -1.301
  254. gendstat: MA1 Kostenki14a -0.311
  255. gendstat: MA1 Tianyuan 0.077
  256. gendstat: MA1 Iran_GanjDareh_N 0.670
  257. gendstat: MA1 Satsurblia_HG -0.196
  258. gendstat: MA1 Pinarbasi -0.299
  259. gendstat: MA1 WSHG1 -0.515
  260. gendstat: MA1 Tagliente_LPaleolithic -1.096
  261. gendstat: MA1 Mongolia_North_N -0.579
  262. gendstat: MA1 Serbia_EN_Starcevo 0.115
  263. gendstat: MA1 Russia_HG_Karelia 1.075
  264. gendstat: Brazil_LapaDoSanto_9600BP Kostenki14a 0.927
  265. gendstat: Brazil_LapaDoSanto_9600BP Tianyuan 1.422
  266. gendstat: Brazil_LapaDoSanto_9600BP Iran_GanjDareh_N 2.236
  267. gendstat: Brazil_LapaDoSanto_9600BP Satsurblia_HG 1.019
  268. gendstat: Brazil_LapaDoSanto_9600BP Pinarbasi 0.905
  269. gendstat: Brazil_LapaDoSanto_9600BP WSHG1 0.700
  270. gendstat: Brazil_LapaDoSanto_9600BP Tagliente_LPaleolithic 0.166
  271. gendstat: Brazil_LapaDoSanto_9600BP Mongolia_North_N 1.030
  272. gendstat: Brazil_LapaDoSanto_9600BP Serbia_EN_Starcevo 1.304
  273. gendstat: Brazil_LapaDoSanto_9600BP Russia_HG_Karelia 2.335
  274. gendstat: Kostenki14a Tianyuan 0.395
  275. gendstat: Kostenki14a Iran_GanjDareh_N 1.040
  276. gendstat: Kostenki14a Satsurblia_HG 0.121
  277. gendstat: Kostenki14a Pinarbasi 0.009
  278. gendstat: Kostenki14a WSHG1 -0.196
  279. gendstat: Kostenki14a Tagliente_LPaleolithic -0.769
  280. gendstat: Kostenki14a Mongolia_North_N -0.232
  281. gendstat: Kostenki14a Serbia_EN_Starcevo 0.429
  282. gendstat: Kostenki14a Russia_HG_Karelia 1.337
  283. gendstat: Tianyuan Iran_GanjDareh_N 0.589
  284. gendstat: Tianyuan Satsurblia_HG -0.272
  285. gendstat: Tianyuan Pinarbasi -0.391
  286. gendstat: Tianyuan WSHG1 -0.557
  287. gendstat: Tianyuan Tagliente_LPaleolithic -1.189
  288. gendstat: Tianyuan Mongolia_North_N -0.745
  289. gendstat: Tianyuan Serbia_EN_Starcevo 0.038
  290. gendstat: Tianyuan Russia_HG_Karelia 0.921
  291. gendstat: Iran_GanjDareh_N Satsurblia_HG -1.044
  292. gendstat: Iran_GanjDareh_N Pinarbasi -1.070
  293. gendstat: Iran_GanjDareh_N WSHG1 -1.173
  294. gendstat: Iran_GanjDareh_N Tagliente_LPaleolithic -2.023
  295. gendstat: Iran_GanjDareh_N Mongolia_North_N -1.526
  296. gendstat: Iran_GanjDareh_N Serbia_EN_Starcevo -0.552
  297. gendstat: Iran_GanjDareh_N Russia_HG_Karelia 0.475
  298. gendstat: Satsurblia_HG Pinarbasi -0.111
  299. gendstat: Satsurblia_HG WSHG1 -0.288
  300. gendstat: Satsurblia_HG Tagliente_LPaleolithic -0.915
  301. gendstat: Satsurblia_HG Mongolia_North_N -0.356
  302. gendstat: Satsurblia_HG Serbia_EN_Starcevo 0.320
  303. gendstat: Satsurblia_HG Russia_HG_Karelia 1.161
  304. gendstat: Pinarbasi WSHG1 -0.187
  305. gendstat: Pinarbasi Tagliente_LPaleolithic -0.751
  306. gendstat: Pinarbasi Mongolia_North_N -0.234
  307. gendstat: Pinarbasi Serbia_EN_Starcevo 0.417
  308. gendstat: Pinarbasi Russia_HG_Karelia 1.293
  309. gendstat: WSHG1 Tagliente_LPaleolithic -0.497
  310. gendstat: WSHG1 Mongolia_North_N 0.002
  311. gendstat: WSHG1 Serbia_EN_Starcevo 0.546
  312. gendstat: WSHG1 Russia_HG_Karelia 1.562
  313. gendstat: Tagliente_LPaleolithic Mongolia_North_N 0.603
  314. gendstat: Tagliente_LPaleolithic Serbia_EN_Starcevo 1.205
  315. gendstat: Tagliente_LPaleolithic Russia_HG_Karelia 2.283
  316. gendstat: Mongolia_North_N Serbia_EN_Starcevo 0.669
  317. gendstat: Mongolia_North_N Russia_HG_Karelia 1.668
  318. gendstat: Serbia_EN_Starcevo Russia_HG_Karelia 0.874
  319.  
  320. ##end of qpAdm: 260.759 seconds cpu 1442.722 Mbytes in use
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