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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: 573491336
  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. Denmark_Djursland_SingleGraveCulture.SG
  22. Sweden_TRB_MN.SG
  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 Denmark_Djursland_SingleGraveCulture.SG 1
  41. 2 Sweden_TRB_MN.SG 3
  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: 1150186 indivs: 33
  57. number of blocks for block jackknife: 714
  58. ## ncols: 1150186
  59. coverage: Sweden_BattleAxe.SG 598273
  60. coverage: Denmark_Djursland_SingleGraveCulture.SG 706074
  61. coverage: Sweden_TRB_MN.SG 757596
  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: 620.037
  76. numsnps used: 1150186
  77. codimension 1
  78. f4info:
  79. f4rank: 1 dof: 11 chisq: 11.692 tail: 0.387267338 dofdiff: 13 chisqdiff: -11.692 taildiff: 1
  80. B:
  81. scale 1.000
  82. Pinarbasi 1.646
  83. MA1 -0.823
  84. Israel_PPNB 1.454
  85. Brazil_LapaDoSanto_9600BP -0.817
  86. Kostenki14a 0.108
  87. Tianyuan 0.094
  88. WSHG1 -1.557
  89. Iran_GanjDareh_N -0.145
  90. Satsurblia_HG -0.201
  91. Mongolia_North_N -0.224
  92. Russia_HG_Karelia -0.648
  93. Serbia_EN_Starcevo 1.690
  94. A:
  95. scale 969.403
  96. Denmark_Djursland_SingleGraveCulture.SG -0.141
  97. Sweden_TRB_MN.SG 1.407
  98.  
  99.  
  100. full rank
  101. f4info:
  102. f4rank: 2 dof: 0 chisq: 0.000 tail: 1 dofdiff: 11 chisqdiff: 11.692 taildiff: 0.387267338
  103. B:
  104. scale 3881.832 692.176
  105. Pinarbasi -0.499 1.635
  106. MA1 -0.613 -0.907
  107. Israel_PPNB -0.243 1.483
  108. Brazil_LapaDoSanto_9600BP 1.604 -0.697
  109. Kostenki14a -0.945 0.027
  110. Tianyuan 1.735 0.289
  111. WSHG1 1.280 -1.529
  112. Iran_GanjDareh_N 0.252 -0.128
  113. Satsurblia_HG 1.008 -0.105
  114. Mongolia_North_N -0.691 -0.294
  115. Russia_HG_Karelia -0.504 -0.722
  116. Serbia_EN_Starcevo -1.177 1.662
  117. A:
  118. scale 1.414 1.414
  119. Denmark_Djursland_SingleGraveCulture.SG 1.414 0.000
  120. Sweden_TRB_MN.SG 0.000 1.414
  121.  
  122.  
  123. best coefficients: 0.909 0.091
  124. Jackknife mean: 0.906342600 0.093657400
  125. std. errors: 0.064 0.064
  126.  
  127. error covariance (* 1,000,000)
  128. 4156 -4156
  129. -4156 4156
  130.  
  131.  
  132. summ: Sweden_BattleAxe.SG 2 0.387267 0.906 0.094 4156 -4156 4156
  133.  
  134. fixed pat wt dof chisq tail prob
  135. 00 0 11 11.692 0.387267 0.909 0.091
  136. 01 1 12 13.682 0.321456 1.000 0.000
  137. 10 1 12 167.537 1.52186e-29 0.000 1.000
  138. best pat: 00 0.387267 - -
  139. best pat: 01 0.321456 chi(nested): 1.991 p-value for nested model: 0.158268
  140.  
  141. coeffs: 0.909 0.091
  142.  
  143. ## dscore:: f_4(Base, Fit, Rbase, right2)
  144. ## genstat:: f_4(Base, Fit, right1, right2)
  145.  
  146. details: Denmark_Djursland_SingleGraveCulture.SG Pinarbasi -0.000129 -0.380015
  147. details: Sweden_TRB_MN.SG Pinarbasi 0.002362 5.604298
  148. dscore: Pinarbasi f4: 0.000098 Z: 0.299512
  149.  
  150. details: Denmark_Djursland_SingleGraveCulture.SG MA1 -0.000158 -0.486413
  151. details: Sweden_TRB_MN.SG MA1 -0.001310 -3.563668
  152. dscore: MA1 f4: -0.000263 Z: -0.846148
  153.  
  154. details: Denmark_Djursland_SingleGraveCulture.SG Israel_PPNB -0.000063 -0.178047
  155. details: Sweden_TRB_MN.SG Israel_PPNB 0.002143 4.966570
  156. dscore: Israel_PPNB f4: 0.000138 Z: 0.406982
  157.  
  158. details: Denmark_Djursland_SingleGraveCulture.SG Brazil_LapaDoSanto_9600BP 0.000413 1.295198
  159. details: Sweden_TRB_MN.SG Brazil_LapaDoSanto_9600BP -0.001007 -2.753915
  160. dscore: Brazil_LapaDoSanto_9600BP f4: 0.000284 Z: 0.925091
  161.  
  162. details: Denmark_Djursland_SingleGraveCulture.SG Kostenki14a -0.000244 -0.732962
  163. details: Sweden_TRB_MN.SG Kostenki14a 0.000040 0.099392
  164. dscore: Kostenki14a f4: -0.000218 Z: -0.674173
  165.  
  166. details: Denmark_Djursland_SingleGraveCulture.SG Tianyuan 0.000447 1.312997
  167. details: Sweden_TRB_MN.SG Tianyuan 0.000417 1.024439
  168. dscore: Tianyuan f4: 0.000444 Z: 1.349334
  169.  
  170. details: Denmark_Djursland_SingleGraveCulture.SG WSHG1 0.000330 0.874069
  171. details: Sweden_TRB_MN.SG WSHG1 -0.002209 -4.918228
  172. dscore: WSHG1 f4: 0.000099 Z: 0.271344
  173.  
  174. details: Denmark_Djursland_SingleGraveCulture.SG Iran_GanjDareh_N 0.000065 0.229592
  175. details: Sweden_TRB_MN.SG Iran_GanjDareh_N -0.000185 -0.580406
  176. dscore: Iran_GanjDareh_N f4: 0.000042 Z: 0.154908
  177.  
  178. details: Denmark_Djursland_SingleGraveCulture.SG Satsurblia_HG 0.000260 0.874174
  179. details: Sweden_TRB_MN.SG Satsurblia_HG -0.000151 -0.455925
  180. dscore: Satsurblia_HG f4: 0.000222 Z: 0.782189
  181.  
  182. details: Denmark_Djursland_SingleGraveCulture.SG Mongolia_North_N -0.000178 -0.585640
  183. details: Sweden_TRB_MN.SG Mongolia_North_N -0.000425 -1.247620
  184. dscore: Mongolia_North_N f4: -0.000200 Z: -0.686265
  185.  
  186. details: Denmark_Djursland_SingleGraveCulture.SG Russia_HG_Karelia -0.000130 -0.380667
  187. details: Sweden_TRB_MN.SG Russia_HG_Karelia -0.001043 -2.633056
  188. dscore: Russia_HG_Karelia f4: -0.000213 Z: -0.647767
  189.  
  190. details: Denmark_Djursland_SingleGraveCulture.SG Serbia_EN_Starcevo -0.000303 -0.866173
  191. details: Sweden_TRB_MN.SG Serbia_EN_Starcevo 0.002401 6.287919
  192. dscore: Serbia_EN_Starcevo f4: -0.000057 Z: -0.172193
  193.  
  194. gendstat: Cameroon_SMA.DG Pinarbasi 0.300
  195. gendstat: Cameroon_SMA.DG MA1 -0.846
  196. gendstat: Cameroon_SMA.DG Israel_PPNB 0.407
  197. gendstat: Cameroon_SMA.DG Brazil_LapaDoSanto_9600BP 0.925
  198. gendstat: Cameroon_SMA.DG Kostenki14a -0.674
  199. gendstat: Cameroon_SMA.DG Tianyuan 1.349
  200. gendstat: Cameroon_SMA.DG WSHG1 0.271
  201. gendstat: Cameroon_SMA.DG Iran_GanjDareh_N 0.155
  202. gendstat: Cameroon_SMA.DG Satsurblia_HG 0.782
  203. gendstat: Cameroon_SMA.DG Mongolia_North_N -0.686
  204. gendstat: Cameroon_SMA.DG Russia_HG_Karelia -0.648
  205. gendstat: Cameroon_SMA.DG Serbia_EN_Starcevo -0.172
  206. gendstat: Pinarbasi MA1 -0.964
  207. gendstat: Pinarbasi Israel_PPNB 0.109
  208. gendstat: Pinarbasi Brazil_LapaDoSanto_9600BP 0.526
  209. gendstat: Pinarbasi Kostenki14a -0.890
  210. gendstat: Pinarbasi Tianyuan 0.901
  211. gendstat: Pinarbasi WSHG1 0.003
  212. gendstat: Pinarbasi Iran_GanjDareh_N -0.176
  213. gendstat: Pinarbasi Satsurblia_HG 0.348
  214. gendstat: Pinarbasi Mongolia_North_N -0.863
  215. gendstat: Pinarbasi Russia_HG_Karelia -0.857
  216. gendstat: Pinarbasi Serbia_EN_Starcevo -0.432
  217. gendstat: MA1 Israel_PPNB 1.051
  218. gendstat: MA1 Brazil_LapaDoSanto_9600BP 1.782
  219. gendstat: MA1 Kostenki14a 0.131
  220. gendstat: MA1 Tianyuan 1.929
  221. gendstat: MA1 WSHG1 1.017
  222. gendstat: MA1 Iran_GanjDareh_N 0.967
  223. gendstat: MA1 Satsurblia_HG 1.414
  224. gendstat: MA1 Mongolia_North_N 0.204
  225. gendstat: MA1 Russia_HG_Karelia 0.151
  226. gendstat: MA1 Serbia_EN_Starcevo 0.520
  227. gendstat: Israel_PPNB Brazil_LapaDoSanto_9600BP 0.408
  228. gendstat: Israel_PPNB Kostenki14a -0.941
  229. gendstat: Israel_PPNB Tianyuan 0.771
  230. gendstat: Israel_PPNB WSHG1 -0.093
  231. gendstat: Israel_PPNB Iran_GanjDareh_N -0.288
  232. gendstat: Israel_PPNB Satsurblia_HG 0.224
  233. gendstat: Israel_PPNB Mongolia_North_N -0.943
  234. gendstat: Israel_PPNB Russia_HG_Karelia -0.910
  235. gendstat: Israel_PPNB Serbia_EN_Starcevo -0.514
  236. gendstat: Brazil_LapaDoSanto_9600BP Kostenki14a -1.541
  237. gendstat: Brazil_LapaDoSanto_9600BP Tianyuan 0.490
  238. gendstat: Brazil_LapaDoSanto_9600BP WSHG1 -0.584
  239. gendstat: Brazil_LapaDoSanto_9600BP Iran_GanjDareh_N -0.876
  240. gendstat: Brazil_LapaDoSanto_9600BP Satsurblia_HG -0.181
  241. gendstat: Brazil_LapaDoSanto_9600BP Mongolia_North_N -2.007
  242. gendstat: Brazil_LapaDoSanto_9600BP Russia_HG_Karelia -1.571
  243. gendstat: Brazil_LapaDoSanto_9600BP Serbia_EN_Starcevo -0.943
  244. gendstat: Kostenki14a Tianyuan 1.888
  245. gendstat: Kostenki14a WSHG1 0.865
  246. gendstat: Kostenki14a Iran_GanjDareh_N 0.870
  247. gendstat: Kostenki14a Satsurblia_HG 1.250
  248. gendstat: Kostenki14a Mongolia_North_N 0.056
  249. gendstat: Kostenki14a Russia_HG_Karelia 0.015
  250. gendstat: Kostenki14a Serbia_EN_Starcevo 0.413
  251. gendstat: Tianyuan WSHG1 -0.918
  252. gendstat: Tianyuan Iran_GanjDareh_N -1.299
  253. gendstat: Tianyuan Satsurblia_HG -0.614
  254. gendstat: Tianyuan Mongolia_North_N -2.164
  255. gendstat: Tianyuan Russia_HG_Karelia -1.740
  256. gendstat: Tianyuan Serbia_EN_Starcevo -1.256
  257. gendstat: WSHG1 Iran_GanjDareh_N -0.173
  258. gendstat: WSHG1 Satsurblia_HG 0.325
  259. gendstat: WSHG1 Mongolia_North_N -0.931
  260. gendstat: WSHG1 Russia_HG_Karelia -0.920
  261. gendstat: WSHG1 Serbia_EN_Starcevo -0.371
  262. gendstat: Iran_GanjDareh_N Satsurblia_HG 0.627
  263. gendstat: Iran_GanjDareh_N Mongolia_North_N -0.915
  264. gendstat: Iran_GanjDareh_N Russia_HG_Karelia -0.829
  265. gendstat: Iran_GanjDareh_N Serbia_EN_Starcevo -0.313
  266. gendstat: Satsurblia_HG Mongolia_North_N -1.312
  267. gendstat: Satsurblia_HG Russia_HG_Karelia -1.285
  268. gendstat: Satsurblia_HG Serbia_EN_Starcevo -0.774
  269. gendstat: Mongolia_North_N Russia_HG_Karelia -0.040
  270. gendstat: Mongolia_North_N Serbia_EN_Starcevo 0.407
  271. gendstat: Russia_HG_Karelia Serbia_EN_Starcevo 0.405
  272.  
  273. ##end of qpAdm: 254.914 seconds cpu 1350.332 Mbytes in use
  274.  
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