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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: 1608000596
  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. Russia_Afanasievo
  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 Russia_Afanasievo 22
  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: 1150155 indivs: 63
  61. number of blocks for block jackknife: 714
  62. ## ncols: 1150155
  63. coverage: Russia_Afanasievo 1122415
  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: 616.834
  82. numsnps used: 1150155
  83. codimension 1
  84. f4info:
  85. f4rank: 2 dof: 11 chisq: 12.220 tail: 0.347325236 dofdiff: 13 chisqdiff: -12.220 taildiff: 1
  86. B:
  87. scale 1.000 1.000
  88. Morocco_Iberomaurusian -0.042 -0.960
  89. MA1 1.289 0.635
  90. Brazil_LapaDoSanto_9600BP 0.988 0.003
  91. Kostenki14a 0.340 1.322
  92. Tianyuan 0.485 0.268
  93. Iran_GanjDareh_N -0.306 1.613
  94. Satsurblia_HG -0.426 1.802
  95. Pinarbasi -0.456 -1.175
  96. WSHG1 2.094 -0.136
  97. Tagliente_LPaleolithic 0.448 -0.263
  98. Mongolia_North_N 0.401 -0.152
  99. Serbia_EN_Starcevo -0.642 -0.983
  100. Russia_HG_Karelia 2.090 -1.246
  101. A:
  102. scale 690.331 3169.310
  103. Russia_Steppe_Eneolithic 0.243 1.603
  104. Russia_Khvalynsk_Eneolithic 1.338 -0.545
  105. Russia_Caucasus_Maikop -1.073 -0.366
  106.  
  107.  
  108. full rank
  109. f4info:
  110. f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 11 chisqdiff: 12.220 taildiff: 0.347325236
  111. B:
  112. scale 1733.795 514.042 609.532
  113. Morocco_Iberomaurusian -1.136 -0.031 -0.022
  114. MA1 1.062 1.153 -1.444
  115. Brazil_LapaDoSanto_9600BP 0.234 0.856 -1.161
  116. Kostenki14a 1.223 0.175 -0.515
  117. Tianyuan 0.776 0.555 -0.418
  118. Iran_GanjDareh_N 1.213 -0.446 0.143
  119. Satsurblia_HG 1.184 -0.659 0.135
  120. Pinarbasi -1.480 -0.370 0.455
  121. WSHG1 1.022 2.010 -2.122
  122. Tagliente_LPaleolithic 0.031 0.424 -0.446
  123. Mongolia_North_N -0.144 0.321 -0.560
  124. Serbia_EN_Starcevo -1.492 -0.604 0.608
  125. Russia_HG_Karelia 0.261 2.267 -1.869
  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: 0.216 0.327 0.457
  134. Jackknife mean: 0.218025554 0.326565898 0.455408548
  135. std. errors: 0.079 0.043 0.043
  136.  
  137. error covariance (* 1,000,000)
  138. 6243 -3110 -3133
  139. -3110 1812 1298
  140. -3133 1298 1835
  141.  
  142.  
  143. summ: Russia_Afanasievo 3 0.347325 0.218 0.327 0.455 6243 -3110 -3133 1812 1298 ...
  144. 1835
  145.  
  146. fixed pat wt dof chisq tail prob
  147. 000 0 11 12.220 0.347325 0.216 0.327 0.457
  148. 001 1 12 71.721 1.52417e-10 1.056 -0.056 0.000 infeasible
  149. 010 1 12 59.472 2.8174e-08 0.799 0.000 0.201
  150. 100 1 12 20.344 0.0608583 0.000 0.432 0.568
  151. 011 2 13 72.289 3.03325e-10 1.000 0.000 0.000
  152. 101 2 13 496.476 0 0.000 1.000 0.000
  153. 110 2 13 360.552 0 0.000 0.000 1.000
  154. best pat: 000 0.347325 - -
  155. best pat: 100 0.0608583 chi(nested): 8.123 p-value for nested model: 0.00436952
  156. best pat: 011 3.03325e-10 not nested
  157.  
  158. coeffs: 0.216 0.327 0.457
  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 -0.000655 -2.714107
  164. details: Russia_Khvalynsk_Eneolithic Morocco_Iberomaurusian -0.000061 -0.259002
  165. details: Russia_Caucasus_Maikop Morocco_Iberomaurusian -0.000036 -0.164469
  166. dscore: Morocco_Iberomaurusian f4: -0.000178 Z: -1.262849
  167.  
  168. details: Russia_Steppe_Eneolithic MA1 0.000613 1.947013
  169. details: Russia_Khvalynsk_Eneolithic MA1 0.002243 7.077310
  170. details: Russia_Caucasus_Maikop MA1 -0.002369 -8.573496
  171. dscore: MA1 f4: -0.000215 Z: -1.150154
  172.  
  173. details: Russia_Steppe_Eneolithic Brazil_LapaDoSanto_9600BP 0.000135 0.476582
  174. details: Russia_Khvalynsk_Eneolithic Brazil_LapaDoSanto_9600BP 0.001665 6.014223
  175. details: Russia_Caucasus_Maikop Brazil_LapaDoSanto_9600BP -0.001905 -7.216779
  176. dscore: Brazil_LapaDoSanto_9600BP f4: -0.000296 Z: -1.773035
  177.  
  178. details: Russia_Steppe_Eneolithic Kostenki14a 0.000706 2.247155
  179. details: Russia_Khvalynsk_Eneolithic Kostenki14a 0.000341 1.115654
  180. details: Russia_Caucasus_Maikop Kostenki14a -0.000846 -3.233027
  181. dscore: Kostenki14a f4: -0.000122 Z: -0.692818
  182.  
  183. details: Russia_Steppe_Eneolithic Tianyuan 0.000448 1.401176
  184. details: Russia_Khvalynsk_Eneolithic Tianyuan 0.001079 3.616308
  185. details: Russia_Caucasus_Maikop Tianyuan -0.000685 -2.512722
  186. dscore: Tianyuan f4: 0.000137 Z: 0.779303
  187.  
  188. details: Russia_Steppe_Eneolithic Iran_GanjDareh_N 0.000700 2.937393
  189. details: Russia_Khvalynsk_Eneolithic Iran_GanjDareh_N -0.000868 -3.640806
  190. details: Russia_Caucasus_Maikop Iran_GanjDareh_N 0.000235 1.058536
  191. dscore: Iran_GanjDareh_N f4: -0.000026 Z: -0.181173
  192.  
  193. details: Russia_Steppe_Eneolithic Satsurblia_HG 0.000683 2.374675
  194. details: Russia_Khvalynsk_Eneolithic Satsurblia_HG -0.001282 -4.244807
  195. details: Russia_Caucasus_Maikop Satsurblia_HG 0.000221 0.829594
  196. dscore: Satsurblia_HG f4: -0.000171 Z: -0.966412
  197.  
  198. details: Russia_Steppe_Eneolithic Pinarbasi -0.000854 -2.883004
  199. details: Russia_Khvalynsk_Eneolithic Pinarbasi -0.000719 -2.310643
  200. details: Russia_Caucasus_Maikop Pinarbasi 0.000747 2.523054
  201. dscore: Pinarbasi f4: -0.000079 Z: -0.408540
  202.  
  203. details: Russia_Steppe_Eneolithic WSHG1 0.000589 1.720230
  204. details: Russia_Khvalynsk_Eneolithic WSHG1 0.003911 11.806431
  205. details: Russia_Caucasus_Maikop WSHG1 -0.003482 -10.775004
  206. dscore: WSHG1 f4: -0.000183 Z: -0.864926
  207.  
  208. details: Russia_Steppe_Eneolithic Tagliente_LPaleolithic 0.000018 0.094523
  209. details: Russia_Khvalynsk_Eneolithic Tagliente_LPaleolithic 0.000826 3.789234
  210. details: Russia_Caucasus_Maikop Tagliente_LPaleolithic -0.000731 -2.793474
  211. dscore: Tagliente_LPaleolithic f4: -0.000060 Z: -0.394628
  212.  
  213. details: Russia_Steppe_Eneolithic Mongolia_North_N -0.000083 -0.316013
  214. details: Russia_Khvalynsk_Eneolithic Mongolia_North_N 0.000625 2.457521
  215. details: Russia_Caucasus_Maikop Mongolia_North_N -0.000918 -3.799814
  216. dscore: Mongolia_North_N f4: -0.000233 Z: -1.523236
  217.  
  218. details: Russia_Steppe_Eneolithic Serbia_EN_Starcevo -0.000861 -2.845547
  219. details: Russia_Khvalynsk_Eneolithic Serbia_EN_Starcevo -0.001175 -3.835828
  220. details: Russia_Caucasus_Maikop Serbia_EN_Starcevo 0.000997 3.505982
  221. dscore: Serbia_EN_Starcevo f4: -0.000115 Z: -0.596989
  222.  
  223. details: Russia_Steppe_Eneolithic Russia_HG_Karelia 0.000150 0.458036
  224. details: Russia_Khvalynsk_Eneolithic Russia_HG_Karelia 0.004410 14.092755
  225. details: Russia_Caucasus_Maikop Russia_HG_Karelia -0.003067 -11.201308
  226. dscore: Russia_HG_Karelia f4: 0.000076 Z: 0.410846
  227.  
  228. gendstat: Cameroon_SMA.DG Morocco_Iberomaurusian -1.263
  229. gendstat: Cameroon_SMA.DG MA1 -1.150
  230. gendstat: Cameroon_SMA.DG Brazil_LapaDoSanto_9600BP -1.773
  231. gendstat: Cameroon_SMA.DG Kostenki14a -0.693
  232. gendstat: Cameroon_SMA.DG Tianyuan 0.779
  233. gendstat: Cameroon_SMA.DG Iran_GanjDareh_N -0.181
  234. gendstat: Cameroon_SMA.DG Satsurblia_HG -0.966
  235. gendstat: Cameroon_SMA.DG Pinarbasi -0.409
  236. gendstat: Cameroon_SMA.DG WSHG1 -0.865
  237. gendstat: Cameroon_SMA.DG Tagliente_LPaleolithic -0.395
  238. gendstat: Cameroon_SMA.DG Mongolia_North_N -1.523
  239. gendstat: Cameroon_SMA.DG Serbia_EN_Starcevo -0.597
  240. gendstat: Cameroon_SMA.DG Russia_HG_Karelia 0.411
  241. gendstat: Morocco_Iberomaurusian MA1 -0.196
  242. gendstat: Morocco_Iberomaurusian Brazil_LapaDoSanto_9600BP -0.705
  243. gendstat: Morocco_Iberomaurusian Kostenki14a 0.296
  244. gendstat: Morocco_Iberomaurusian Tianyuan 1.693
  245. gendstat: Morocco_Iberomaurusian Iran_GanjDareh_N 0.997
  246. gendstat: Morocco_Iberomaurusian Satsurblia_HG 0.033
  247. gendstat: Morocco_Iberomaurusian Pinarbasi 0.520
  248. gendstat: Morocco_Iberomaurusian WSHG1 -0.024
  249. gendstat: Morocco_Iberomaurusian Tagliente_LPaleolithic 0.633
  250. gendstat: Morocco_Iberomaurusian Mongolia_North_N -0.342
  251. gendstat: Morocco_Iberomaurusian Serbia_EN_Starcevo 0.325
  252. gendstat: Morocco_Iberomaurusian Russia_HG_Karelia 1.370
  253. gendstat: MA1 Brazil_LapaDoSanto_9600BP -0.419
  254. gendstat: MA1 Kostenki14a 0.439
  255. gendstat: MA1 Tianyuan 1.689
  256. gendstat: MA1 Iran_GanjDareh_N 1.039
  257. gendstat: MA1 Satsurblia_HG 0.198
  258. gendstat: MA1 Pinarbasi 0.601
  259. gendstat: MA1 WSHG1 0.150
  260. gendstat: MA1 Tagliente_LPaleolithic 0.704
  261. gendstat: MA1 Mongolia_North_N -0.094
  262. gendstat: MA1 Serbia_EN_Starcevo 0.454
  263. gendstat: MA1 Russia_HG_Karelia 1.436
  264. gendstat: Brazil_LapaDoSanto_9600BP Kostenki14a 0.916
  265. gendstat: Brazil_LapaDoSanto_9600BP Tianyuan 2.368
  266. gendstat: Brazil_LapaDoSanto_9600BP Iran_GanjDareh_N 1.679
  267. gendstat: Brazil_LapaDoSanto_9600BP Satsurblia_HG 0.596
  268. gendstat: Brazil_LapaDoSanto_9600BP Pinarbasi 1.074
  269. gendstat: Brazil_LapaDoSanto_9600BP WSHG1 0.564
  270. gendstat: Brazil_LapaDoSanto_9600BP Tagliente_LPaleolithic 1.187
  271. gendstat: Brazil_LapaDoSanto_9600BP Mongolia_North_N 0.479
  272. gendstat: Brazil_LapaDoSanto_9600BP Serbia_EN_Starcevo 0.916
  273. gendstat: Brazil_LapaDoSanto_9600BP Russia_HG_Karelia 2.028
  274. gendstat: Kostenki14a Tianyuan 1.290
  275. gendstat: Kostenki14a Iran_GanjDareh_N 0.530
  276. gendstat: Kostenki14a Satsurblia_HG -0.229
  277. gendstat: Kostenki14a Pinarbasi 0.201
  278. gendstat: Kostenki14a WSHG1 -0.267
  279. gendstat: Kostenki14a Tagliente_LPaleolithic 0.288
  280. gendstat: Kostenki14a Mongolia_North_N -0.615
  281. gendstat: Kostenki14a Serbia_EN_Starcevo 0.035
  282. gendstat: Kostenki14a Russia_HG_Karelia 0.973
  283. gendstat: Tianyuan Iran_GanjDareh_N -0.907
  284. gendstat: Tianyuan Satsurblia_HG -1.408
  285. gendstat: Tianyuan Pinarbasi -0.951
  286. gendstat: Tianyuan WSHG1 -1.366
  287. gendstat: Tianyuan Tagliente_LPaleolithic -0.939
  288. gendstat: Tianyuan Mongolia_North_N -2.270
  289. gendstat: Tianyuan Serbia_EN_Starcevo -1.175
  290. gendstat: Tianyuan Russia_HG_Karelia -0.304
  291. gendstat: Iran_GanjDareh_N Satsurblia_HG -0.856
  292. gendstat: Iran_GanjDareh_N Pinarbasi -0.289
  293. gendstat: Iran_GanjDareh_N WSHG1 -0.770
  294. gendstat: Iran_GanjDareh_N Tagliente_LPaleolithic -0.184
  295. gendstat: Iran_GanjDareh_N Mongolia_North_N -1.444
  296. gendstat: Iran_GanjDareh_N Serbia_EN_Starcevo -0.488
  297. gendstat: Iran_GanjDareh_N Russia_HG_Karelia 0.556
  298. gendstat: Satsurblia_HG Pinarbasi 0.417
  299. gendstat: Satsurblia_HG WSHG1 -0.047
  300. gendstat: Satsurblia_HG Tagliente_LPaleolithic 0.510
  301. gendstat: Satsurblia_HG Mongolia_North_N -0.317
  302. gendstat: Satsurblia_HG Serbia_EN_Starcevo 0.257
  303. gendstat: Satsurblia_HG Russia_HG_Karelia 1.105
  304. gendstat: Pinarbasi WSHG1 -0.435
  305. gendstat: Pinarbasi Tagliente_LPaleolithic 0.087
  306. gendstat: Pinarbasi Mongolia_North_N -0.819
  307. gendstat: Pinarbasi Serbia_EN_Starcevo -0.175
  308. gendstat: Pinarbasi Russia_HG_Karelia 0.740
  309. gendstat: WSHG1 Tagliente_LPaleolithic 0.523
  310. gendstat: WSHG1 Mongolia_North_N -0.253
  311. gendstat: WSHG1 Serbia_EN_Starcevo 0.272
  312. gendstat: WSHG1 Russia_HG_Karelia 1.317
  313. gendstat: Tagliente_LPaleolithic Mongolia_North_N -0.917
  314. gendstat: Tagliente_LPaleolithic Serbia_EN_Starcevo -0.255
  315. gendstat: Tagliente_LPaleolithic Russia_HG_Karelia 0.663
  316. gendstat: Mongolia_North_N Serbia_EN_Starcevo 0.620
  317. gendstat: Mongolia_North_N Russia_HG_Karelia 1.761
  318. gendstat: Serbia_EN_Starcevo Russia_HG_Karelia 0.847
  319.  
  320. ##end of qpAdm: 269.240 seconds cpu 1442.738 Mbytes in use
  321.  
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