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RG701
Jul 16th, 2022 (edited)
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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: 1608723598
  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. Ukraine_Globular_Amphora
  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 Ukraine_Globular_Amphora 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: 1150142 indivs: 47
  61. number of blocks for block jackknife: 714
  62. ## ncols: 1150142
  63. coverage: Yam_Samara 1027282
  64. coverage: Russia_Steppe_Eneolithic 952133
  65. coverage: Russia_Khvalynsk_Eneolithic 758497
  66. coverage: Ukraine_Globular_Amphora 985542
  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: 616.464
  82. numsnps used: 1150142
  83. codimension 1
  84. f4info:
  85. f4rank: 2 dof: 11 chisq: 9.750 tail: 0.553037783 dofdiff: 13 chisqdiff: -9.750 taildiff: 1
  86. B:
  87. scale 1.000 1.000
  88. Morocco_Iberomaurusian -0.358 0.815
  89. MA1 1.267 -0.071
  90. Brazil_LapaDoSanto_9600BP 0.990 -0.023
  91. Kostenki14a -0.020 0.075
  92. Tianyuan 0.506 0.118
  93. Iran_GanjDareh_N 0.423 -1.528
  94. Satsurblia_HG 0.436 -1.814
  95. Pinarbasi -1.172 1.392
  96. WSHG1 1.936 0.526
  97. Tagliente_LPaleolithic -0.121 0.557
  98. Mongolia_North_N 0.538 -0.069
  99. Serbia_EN_Starcevo -1.211 1.078
  100. Russia_HG_Karelia 1.664 1.730
  101. A:
  102. scale 459.579 1676.496
  103. Russia_Steppe_Eneolithic 0.102 -0.629
  104. Russia_Khvalynsk_Eneolithic 0.744 1.476
  105. Ukraine_Globular_Amphora -1.561 0.653
  106.  
  107.  
  108. full rank
  109. f4info:
  110. f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 11 chisqdiff: 9.750 taildiff: 0.553037783
  111. B:
  112. scale 2081.225 549.611 292.443
  113. Morocco_Iberomaurusian -1.082 0.086 0.453
  114. MA1 1.032 1.163 -1.218
  115. Brazil_LapaDoSanto_9600BP -0.122 0.792 -1.013
  116. Kostenki14a 1.131 0.202 0.141
  117. Tianyuan 0.263 0.500 -0.482
  118. Iran_GanjDareh_N 1.562 -0.314 -0.562
  119. Satsurblia_HG 1.409 -0.504 -0.641
  120. Pinarbasi -1.617 -0.342 1.328
  121. WSHG1 0.629 2.014 -1.844
  122. Tagliente_LPaleolithic -0.386 0.185 0.197
  123. Mongolia_North_N -0.162 0.389 -0.552
  124. Serbia_EN_Starcevo -1.328 -0.476 1.349
  125. Russia_HG_Karelia -0.172 2.405 -1.407
  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. Ukraine_Globular_Amphora 0.000 0.000 1.732
  131.  
  132.  
  133. best coefficients: 0.645 0.212 0.143
  134. Jackknife mean: 0.642997123 0.213746480 0.143256398
  135. std. errors: 0.058 0.049 0.020
  136.  
  137. error covariance (* 1,000,000)
  138. 3416 -2691 -725
  139. -2691 2382 309
  140. -725 309 415
  141.  
  142.  
  143. summ: Yam_Samara 3 0.553038 0.643 0.214 0.143 3416 -2691 -725 2382 309 ...
  144. 415
  145.  
  146. fixed pat wt dof chisq tail prob
  147. 000 0 11 9.750 0.553038 0.645 0.212 0.143
  148. 001 1 12 46.291 6.17963e-06 0.961 0.039 0.000
  149. 010 1 12 24.656 0.0165383 0.886 0.000 0.114
  150. 100 1 12 146.517 2.88082e-25 0.000 0.713 0.287
  151. 011 2 13 46.725 1.07506e-05 1.000 0.000 0.000
  152. 101 2 13 362.710 0 0.000 1.000 0.000
  153. 110 2 13 1078.522 0 0.000 0.000 1.000
  154. best pat: 000 0.553038 - -
  155. best pat: 010 0.0165383 chi(nested): 14.907 p-value for nested model: 0.000112964
  156. best pat: 011 1.07506e-05 chi(nested): 22.069 p-value for nested model: 2.63052e-06
  157.  
  158. coeffs: 0.645 0.212 0.143
  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 -1.797516
  164. details: Russia_Khvalynsk_Eneolithic Morocco_Iberomaurusian 0.000156 0.622076
  165. details: Ukraine_Globular_Amphora Morocco_Iberomaurusian 0.001550 5.144424
  166. dscore: Morocco_Iberomaurusian f4: -0.000081 Z: -0.354734
  167.  
  168. details: Russia_Steppe_Eneolithic MA1 0.000496 1.445147
  169. details: Russia_Khvalynsk_Eneolithic MA1 0.002115 6.662171
  170. details: Ukraine_Globular_Amphora MA1 -0.004166 -11.411408
  171. dscore: MA1 f4: 0.000171 Z: 0.631629
  172.  
  173. details: Russia_Steppe_Eneolithic Brazil_LapaDoSanto_9600BP -0.000059 -0.171366
  174. details: Russia_Khvalynsk_Eneolithic Brazil_LapaDoSanto_9600BP 0.001441 4.723747
  175. details: Ukraine_Globular_Amphora Brazil_LapaDoSanto_9600BP -0.003463 -10.373306
  176. dscore: Brazil_LapaDoSanto_9600BP f4: -0.000228 Z: -0.838342
  177.  
  178. details: Russia_Steppe_Eneolithic Kostenki14a 0.000543 1.536582
  179. details: Russia_Khvalynsk_Eneolithic Kostenki14a 0.000368 1.138002
  180. details: Ukraine_Globular_Amphora Kostenki14a 0.000482 1.225837
  181. dscore: Kostenki14a f4: 0.000497 Z: 1.794201
  182.  
  183. details: Russia_Steppe_Eneolithic Tianyuan 0.000126 0.351077
  184. details: Russia_Khvalynsk_Eneolithic Tianyuan 0.000910 2.946688
  185. details: Ukraine_Globular_Amphora Tianyuan -0.001649 -4.312335
  186. dscore: Tianyuan f4: 0.000038 Z: 0.135899
  187.  
  188. details: Russia_Steppe_Eneolithic Iran_GanjDareh_N 0.000750 2.644848
  189. details: Russia_Khvalynsk_Eneolithic Iran_GanjDareh_N -0.000571 -2.132339
  190. details: Ukraine_Globular_Amphora Iran_GanjDareh_N -0.001921 -6.648027
  191. dscore: Iran_GanjDareh_N f4: 0.000088 Z: 0.384943
  192.  
  193. details: Russia_Steppe_Eneolithic Satsurblia_HG 0.000677 2.134281
  194. details: Russia_Khvalynsk_Eneolithic Satsurblia_HG -0.000917 -2.949471
  195. details: Ukraine_Globular_Amphora Satsurblia_HG -0.002193 -6.512957
  196. dscore: Satsurblia_HG f4: -0.000071 Z: -0.278612
  197.  
  198. details: Russia_Steppe_Eneolithic Pinarbasi -0.000777 -2.219629
  199. details: Russia_Khvalynsk_Eneolithic Pinarbasi -0.000621 -1.837549
  200. details: Ukraine_Globular_Amphora Pinarbasi 0.004542 11.584779
  201. dscore: Pinarbasi f4: 0.000017 Z: 0.061232
  202.  
  203. details: Russia_Steppe_Eneolithic WSHG1 0.000302 0.806284
  204. details: Russia_Khvalynsk_Eneolithic WSHG1 0.003665 10.489616
  205. details: Ukraine_Globular_Amphora WSHG1 -0.006305 -16.077971
  206. dscore: WSHG1 f4: 0.000069 Z: 0.235002
  207.  
  208. details: Russia_Steppe_Eneolithic Tagliente_LPaleolithic -0.000186 -1.125653
  209. details: Russia_Khvalynsk_Eneolithic Tagliente_LPaleolithic 0.000337 1.874348
  210. details: Ukraine_Globular_Amphora Tagliente_LPaleolithic 0.000673 3.683004
  211. dscore: Tagliente_LPaleolithic f4: 0.000048 Z: 0.358263
  212.  
  213. details: Russia_Steppe_Eneolithic Mongolia_North_N -0.000078 -0.250432
  214. details: Russia_Khvalynsk_Eneolithic Mongolia_North_N 0.000707 2.531866
  215. details: Ukraine_Globular_Amphora Mongolia_North_N -0.001888 -6.015879
  216. dscore: Mongolia_North_N f4: -0.000171 Z: -0.699198
  217.  
  218. details: Russia_Steppe_Eneolithic Serbia_EN_Starcevo -0.000638 -1.889823
  219. details: Russia_Khvalynsk_Eneolithic Serbia_EN_Starcevo -0.000867 -2.651961
  220. details: Ukraine_Globular_Amphora Serbia_EN_Starcevo 0.004613 12.749197
  221. dscore: Serbia_EN_Starcevo f4: 0.000065 Z: 0.242375
  222.  
  223. details: Russia_Steppe_Eneolithic Russia_HG_Karelia -0.000083 -0.222388
  224. details: Russia_Khvalynsk_Eneolithic Russia_HG_Karelia 0.004375 13.094813
  225. details: Ukraine_Globular_Amphora Russia_HG_Karelia -0.004810 -11.953161
  226. dscore: Russia_HG_Karelia f4: 0.000185 Z: 0.629112
  227.  
  228. gendstat: Cameroon_SMA.DG Morocco_Iberomaurusian -0.355
  229. gendstat: Cameroon_SMA.DG MA1 0.632
  230. gendstat: Cameroon_SMA.DG Brazil_LapaDoSanto_9600BP -0.838
  231. gendstat: Cameroon_SMA.DG Kostenki14a 1.794
  232. gendstat: Cameroon_SMA.DG Tianyuan 0.136
  233. gendstat: Cameroon_SMA.DG Iran_GanjDareh_N 0.385
  234. gendstat: Cameroon_SMA.DG Satsurblia_HG -0.279
  235. gendstat: Cameroon_SMA.DG Pinarbasi 0.061
  236. gendstat: Cameroon_SMA.DG WSHG1 0.235
  237. gendstat: Cameroon_SMA.DG Tagliente_LPaleolithic 0.358
  238. gendstat: Cameroon_SMA.DG Mongolia_North_N -0.699
  239. gendstat: Cameroon_SMA.DG Serbia_EN_Starcevo 0.242
  240. gendstat: Cameroon_SMA.DG Russia_HG_Karelia 0.629
  241. gendstat: Morocco_Iberomaurusian MA1 0.874
  242. gendstat: Morocco_Iberomaurusian Brazil_LapaDoSanto_9600BP -0.546
  243. gendstat: Morocco_Iberomaurusian Kostenki14a 2.113
  244. gendstat: Morocco_Iberomaurusian Tianyuan 0.419
  245. gendstat: Morocco_Iberomaurusian Iran_GanjDareh_N 0.728
  246. gendstat: Morocco_Iberomaurusian Satsurblia_HG 0.033
  247. gendstat: Morocco_Iberomaurusian Pinarbasi 0.358
  248. gendstat: Morocco_Iberomaurusian WSHG1 0.489
  249. gendstat: Morocco_Iberomaurusian Tagliente_LPaleolithic 0.540
  250. gendstat: Morocco_Iberomaurusian Mongolia_North_N -0.382
  251. gendstat: Morocco_Iberomaurusian Serbia_EN_Starcevo 0.560
  252. gendstat: Morocco_Iberomaurusian Russia_HG_Karelia 0.887
  253. gendstat: MA1 Brazil_LapaDoSanto_9600BP -1.444
  254. gendstat: MA1 Kostenki14a 1.081
  255. gendstat: MA1 Tianyuan -0.420
  256. gendstat: MA1 Iran_GanjDareh_N -0.299
  257. gendstat: MA1 Satsurblia_HG -0.788
  258. gendstat: MA1 Pinarbasi -0.484
  259. gendstat: MA1 WSHG1 -0.354
  260. gendstat: MA1 Tagliente_LPaleolithic -0.445
  261. gendstat: MA1 Mongolia_North_N -1.298
  262. gendstat: MA1 Serbia_EN_Starcevo -0.333
  263. gendstat: MA1 Russia_HG_Karelia 0.045
  264. gendstat: Brazil_LapaDoSanto_9600BP Kostenki14a 2.512
  265. gendstat: Brazil_LapaDoSanto_9600BP Tianyuan 0.942
  266. gendstat: Brazil_LapaDoSanto_9600BP Iran_GanjDareh_N 1.273
  267. gendstat: Brazil_LapaDoSanto_9600BP Satsurblia_HG 0.515
  268. gendstat: Brazil_LapaDoSanto_9600BP Pinarbasi 0.812
  269. gendstat: Brazil_LapaDoSanto_9600BP WSHG1 1.044
  270. gendstat: Brazil_LapaDoSanto_9600BP Tagliente_LPaleolithic 1.016
  271. gendstat: Brazil_LapaDoSanto_9600BP Mongolia_North_N 0.287
  272. gendstat: Brazil_LapaDoSanto_9600BP Serbia_EN_Starcevo 0.953
  273. gendstat: Brazil_LapaDoSanto_9600BP Russia_HG_Karelia 1.387
  274. gendstat: Kostenki14a Tianyuan -1.497
  275. gendstat: Kostenki14a Iran_GanjDareh_N -1.518
  276. gendstat: Kostenki14a Satsurblia_HG -1.832
  277. gendstat: Kostenki14a Pinarbasi -1.574
  278. gendstat: Kostenki14a WSHG1 -1.378
  279. gendstat: Kostenki14a Tagliente_LPaleolithic -1.629
  280. gendstat: Kostenki14a Mongolia_North_N -2.552
  281. gendstat: Kostenki14a Serbia_EN_Starcevo -1.389
  282. gendstat: Kostenki14a Russia_HG_Karelia -0.985
  283. gendstat: Tianyuan Iran_GanjDareh_N 0.185
  284. gendstat: Tianyuan Satsurblia_HG -0.343
  285. gendstat: Tianyuan Pinarbasi -0.065
  286. gendstat: Tianyuan WSHG1 0.093
  287. gendstat: Tianyuan Tagliente_LPaleolithic 0.035
  288. gendstat: Tianyuan Mongolia_North_N -0.843
  289. gendstat: Tianyuan Serbia_EN_Starcevo 0.083
  290. gendstat: Tianyuan Russia_HG_Karelia 0.436
  291. gendstat: Iran_GanjDareh_N Satsurblia_HG -0.658
  292. gendstat: Iran_GanjDareh_N Pinarbasi -0.272
  293. gendstat: Iran_GanjDareh_N WSHG1 -0.066
  294. gendstat: Iran_GanjDareh_N Tagliente_LPaleolithic -0.167
  295. gendstat: Iran_GanjDareh_N Mongolia_North_N -1.202
  296. gendstat: Iran_GanjDareh_N Serbia_EN_Starcevo -0.089
  297. gendstat: Iran_GanjDareh_N Russia_HG_Karelia 0.317
  298. gendstat: Satsurblia_HG Pinarbasi 0.293
  299. gendstat: Satsurblia_HG WSHG1 0.413
  300. gendstat: Satsurblia_HG Tagliente_LPaleolithic 0.436
  301. gendstat: Satsurblia_HG Mongolia_North_N -0.366
  302. gendstat: Satsurblia_HG Serbia_EN_Starcevo 0.451
  303. gendstat: Satsurblia_HG Russia_HG_Karelia 0.743
  304. gendstat: Pinarbasi WSHG1 0.153
  305. gendstat: Pinarbasi Tagliente_LPaleolithic 0.106
  306. gendstat: Pinarbasi Mongolia_North_N -0.710
  307. gendstat: Pinarbasi Serbia_EN_Starcevo 0.159
  308. gendstat: Pinarbasi Russia_HG_Karelia 0.498
  309. gendstat: WSHG1 Tagliente_LPaleolithic -0.070
  310. gendstat: WSHG1 Mongolia_North_N -0.867
  311. gendstat: WSHG1 Serbia_EN_Starcevo -0.011
  312. gendstat: WSHG1 Russia_HG_Karelia 0.376
  313. gendstat: Tagliente_LPaleolithic Mongolia_North_N -0.891
  314. gendstat: Tagliente_LPaleolithic Serbia_EN_Starcevo 0.062
  315. gendstat: Tagliente_LPaleolithic Russia_HG_Karelia 0.466
  316. gendstat: Mongolia_North_N Serbia_EN_Starcevo 0.831
  317. gendstat: Mongolia_North_N Russia_HG_Karelia 1.200
  318. gendstat: Serbia_EN_Starcevo Russia_HG_Karelia 0.361
  319.  
  320. ##end of qpAdm: 261.901 seconds cpu 1442.730 Mbytes in use
  321.  
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