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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: 573295080
  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. Estonia_CordedWare.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 Estonia_CordedWare.SG 3
  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: 1150224 indivs: 35
  57. number of blocks for block jackknife: 714
  58. ## ncols: 1150224
  59. coverage: Sweden_BattleAxe.SG 598273
  60. coverage: Estonia_CordedWare.SG 1040582
  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: 621.388
  76. numsnps used: 1150224
  77. codimension 1
  78. f4info:
  79. f4rank: 1 dof: 11 chisq: 6.403 tail: 0.845154304 dofdiff: 13 chisqdiff: -6.403 taildiff: 1
  80. B:
  81. scale 1.000
  82. Pinarbasi 1.598
  83. MA1 -0.852
  84. Israel_PPNB 1.654
  85. Brazil_LapaDoSanto_9600BP -0.656
  86. Kostenki14a 0.262
  87. Tianyuan 0.180
  88. WSHG1 -1.341
  89. Iran_GanjDareh_N -0.193
  90. Satsurblia_HG -0.216
  91. Mongolia_North_N -0.253
  92. Russia_HG_Karelia -0.713
  93. Serbia_EN_Starcevo 1.732
  94. A:
  95. scale 954.965
  96. Estonia_CordedWare.SG -0.362
  97. Sweden_TRB_MN.SG 1.367
  98.  
  99.  
  100. full rank
  101. f4info:
  102. f4rank: 2 dof: 0 chisq: 0.000 tail: 1 dofdiff: 11 chisqdiff: 6.403 taildiff: 0.845154304
  103. B:
  104. scale 2275.571 692.176
  105. Pinarbasi -1.242 1.635
  106. MA1 0.504 -0.907
  107. Israel_PPNB -2.049 1.483
  108. Brazil_LapaDoSanto_9600BP 0.383 -0.697
  109. Kostenki14a -1.224 0.027
  110. Tianyuan 0.362 0.289
  111. WSHG1 0.336 -1.529
  112. Iran_GanjDareh_N 0.337 -0.128
  113. Satsurblia_HG 0.634 -0.105
  114. Mongolia_North_N -0.044 -0.294
  115. Russia_HG_Karelia 0.497 -0.722
  116. Serbia_EN_Starcevo -1.831 1.662
  117. A:
  118. scale 1.414 1.414
  119. Estonia_CordedWare.SG 1.414 0.000
  120. Sweden_TRB_MN.SG 0.000 1.414
  121.  
  122.  
  123. best coefficients: 0.790 0.210
  124. Jackknife mean: 0.789489384 0.210510616
  125. std. errors: 0.058 0.058
  126.  
  127. error covariance (* 1,000,000)
  128. 3317 -3317
  129. -3317 3317
  130.  
  131.  
  132. summ: Sweden_BattleAxe.SG 2 0.845154 0.789 0.211 3317 -3317 3317
  133.  
  134. fixed pat wt dof chisq tail prob
  135. 00 0 11 6.403 0.845154 0.790 0.210
  136. 01 1 12 18.268 0.10778 1.000 0.000
  137. 10 1 12 168.083 1.17726e-29 0.000 1.000
  138. best pat: 00 0.845154 - -
  139. best pat: 01 0.10778 chi(nested): 11.865 p-value for nested model: 0.000571916
  140.  
  141. coeffs: 0.790 0.210
  142.  
  143. ## dscore:: f_4(Base, Fit, Rbase, right2)
  144. ## genstat:: f_4(Base, Fit, right1, right2)
  145.  
  146. details: Estonia_CordedWare.SG Pinarbasi -0.000546 -1.475707
  147. details: Sweden_TRB_MN.SG Pinarbasi 0.002362 5.618743
  148. dscore: Pinarbasi f4: 0.000064 Z: 0.181252
  149.  
  150. details: Estonia_CordedWare.SG MA1 0.000221 0.624775
  151. details: Sweden_TRB_MN.SG MA1 -0.001310 -3.571423
  152. dscore: MA1 f4: -0.000099 Z: -0.302280
  153.  
  154. details: Estonia_CordedWare.SG Israel_PPNB -0.000900 -2.304518
  155. details: Sweden_TRB_MN.SG Israel_PPNB 0.002143 4.980939
  156. dscore: Israel_PPNB f4: -0.000263 Z: -0.709948
  157.  
  158. details: Estonia_CordedWare.SG Brazil_LapaDoSanto_9600BP 0.000168 0.493302
  159. details: Sweden_TRB_MN.SG Brazil_LapaDoSanto_9600BP -0.001007 -2.759714
  160. dscore: Brazil_LapaDoSanto_9600BP f4: -0.000078 Z: -0.244355
  161.  
  162. details: Estonia_CordedWare.SG Kostenki14a -0.000538 -1.421206
  163. details: Sweden_TRB_MN.SG Kostenki14a 0.000040 0.099696
  164. dscore: Kostenki14a f4: -0.000417 Z: -1.170700
  165.  
  166. details: Estonia_CordedWare.SG Tianyuan 0.000159 0.445898
  167. details: Sweden_TRB_MN.SG Tianyuan 0.000417 1.026702
  168. dscore: Tianyuan f4: 0.000213 Z: 0.634744
  169.  
  170. details: Estonia_CordedWare.SG WSHG1 0.000148 0.358646
  171. details: Sweden_TRB_MN.SG WSHG1 -0.002209 -4.930799
  172. dscore: WSHG1 f4: -0.000346 Z: -0.892235
  173.  
  174. details: Estonia_CordedWare.SG Iran_GanjDareh_N 0.000148 0.508539
  175. details: Sweden_TRB_MN.SG Iran_GanjDareh_N -0.000185 -0.581677
  176. dscore: Iran_GanjDareh_N f4: 0.000078 Z: 0.286269
  177.  
  178. details: Estonia_CordedWare.SG Satsurblia_HG 0.000279 0.900459
  179. details: Sweden_TRB_MN.SG Satsurblia_HG -0.000151 -0.456748
  180. dscore: Satsurblia_HG f4: 0.000189 Z: 0.650986
  181.  
  182. details: Estonia_CordedWare.SG Mongolia_North_N -0.000019 -0.061029
  183. details: Sweden_TRB_MN.SG Mongolia_North_N -0.000425 -1.251117
  184. dscore: Mongolia_North_N f4: -0.000104 Z: -0.354210
  185.  
  186. details: Estonia_CordedWare.SG Russia_HG_Karelia 0.000218 0.587102
  187. details: Sweden_TRB_MN.SG Russia_HG_Karelia -0.001043 -2.638600
  188. dscore: Russia_HG_Karelia f4: -0.000046 Z: -0.131102
  189.  
  190. details: Estonia_CordedWare.SG Serbia_EN_Starcevo -0.000805 -2.142895
  191. details: Sweden_TRB_MN.SG Serbia_EN_Starcevo 0.002401 6.298198
  192. dscore: Serbia_EN_Starcevo f4: -0.000133 Z: -0.384912
  193.  
  194. gendstat: Cameroon_SMA.DG Pinarbasi 0.181
  195. gendstat: Cameroon_SMA.DG MA1 -0.302
  196. gendstat: Cameroon_SMA.DG Israel_PPNB -0.710
  197. gendstat: Cameroon_SMA.DG Brazil_LapaDoSanto_9600BP -0.244
  198. gendstat: Cameroon_SMA.DG Kostenki14a -1.171
  199. gendstat: Cameroon_SMA.DG Tianyuan 0.635
  200. gendstat: Cameroon_SMA.DG WSHG1 -0.892
  201. gendstat: Cameroon_SMA.DG Iran_GanjDareh_N 0.286
  202. gendstat: Cameroon_SMA.DG Satsurblia_HG 0.651
  203. gendstat: Cameroon_SMA.DG Mongolia_North_N -0.354
  204. gendstat: Cameroon_SMA.DG Russia_HG_Karelia -0.131
  205. gendstat: Cameroon_SMA.DG Serbia_EN_Starcevo -0.385
  206. gendstat: Pinarbasi MA1 -0.406
  207. gendstat: Pinarbasi Israel_PPNB -0.828
  208. gendstat: Pinarbasi Brazil_LapaDoSanto_9600BP -0.386
  209. gendstat: Pinarbasi Kostenki14a -1.260
  210. gendstat: Pinarbasi Tianyuan 0.371
  211. gendstat: Pinarbasi WSHG1 -0.948
  212. gendstat: Pinarbasi Iran_GanjDareh_N 0.045
  213. gendstat: Pinarbasi Satsurblia_HG 0.328
  214. gendstat: Pinarbasi Mongolia_North_N -0.493
  215. gendstat: Pinarbasi Russia_HG_Karelia -0.277
  216. gendstat: Pinarbasi Serbia_EN_Starcevo -0.516
  217. gendstat: MA1 Israel_PPNB -0.394
  218. gendstat: MA1 Brazil_LapaDoSanto_9600BP 0.064
  219. gendstat: MA1 Kostenki14a -0.809
  220. gendstat: MA1 Tianyuan 0.819
  221. gendstat: MA1 WSHG1 -0.653
  222. gendstat: MA1 Iran_GanjDareh_N 0.547
  223. gendstat: MA1 Satsurblia_HG 0.788
  224. gendstat: MA1 Mongolia_North_N -0.015
  225. gendstat: MA1 Russia_HG_Karelia 0.146
  226. gendstat: MA1 Serbia_EN_Starcevo -0.081
  227. gendstat: Israel_PPNB Brazil_LapaDoSanto_9600BP 0.470
  228. gendstat: Israel_PPNB Kostenki14a -0.369
  229. gendstat: Israel_PPNB Tianyuan 1.122
  230. gendstat: Israel_PPNB WSHG1 -0.179
  231. gendstat: Israel_PPNB Iran_GanjDareh_N 0.960
  232. gendstat: Israel_PPNB Satsurblia_HG 1.109
  233. gendstat: Israel_PPNB Mongolia_North_N 0.435
  234. gendstat: Israel_PPNB Russia_HG_Karelia 0.510
  235. gendstat: Israel_PPNB Serbia_EN_Starcevo 0.329
  236. gendstat: Brazil_LapaDoSanto_9600BP Kostenki14a -0.949
  237. gendstat: Brazil_LapaDoSanto_9600BP Tianyuan 0.866
  238. gendstat: Brazil_LapaDoSanto_9600BP WSHG1 -0.746
  239. gendstat: Brazil_LapaDoSanto_9600BP Iran_GanjDareh_N 0.542
  240. gendstat: Brazil_LapaDoSanto_9600BP Satsurblia_HG 0.747
  241. gendstat: Brazil_LapaDoSanto_9600BP Mongolia_North_N -0.105
  242. gendstat: Brazil_LapaDoSanto_9600BP Russia_HG_Karelia 0.096
  243. gendstat: Brazil_LapaDoSanto_9600BP Serbia_EN_Starcevo -0.144
  244. gendstat: Kostenki14a Tianyuan 1.706
  245. gendstat: Kostenki14a WSHG1 0.175
  246. gendstat: Kostenki14a Iran_GanjDareh_N 1.528
  247. gendstat: Kostenki14a Satsurblia_HG 1.623
  248. gendstat: Kostenki14a Mongolia_North_N 0.941
  249. gendstat: Kostenki14a Russia_HG_Karelia 0.998
  250. gendstat: Kostenki14a Serbia_EN_Starcevo 0.689
  251. gendstat: Tianyuan WSHG1 -1.385
  252. gendstat: Tianyuan Iran_GanjDareh_N -0.423
  253. gendstat: Tianyuan Satsurblia_HG -0.065
  254. gendstat: Tianyuan Mongolia_North_N -1.034
  255. gendstat: Tianyuan Russia_HG_Karelia -0.657
  256. gendstat: Tianyuan Serbia_EN_Starcevo -0.813
  257. gendstat: WSHG1 Iran_GanjDareh_N 1.189
  258. gendstat: WSHG1 Satsurblia_HG 1.325
  259. gendstat: WSHG1 Mongolia_North_N 0.672
  260. gendstat: WSHG1 Russia_HG_Karelia 0.823
  261. gendstat: WSHG1 Serbia_EN_Starcevo 0.469
  262. gendstat: Iran_GanjDareh_N Satsurblia_HG 0.372
  263. gendstat: Iran_GanjDareh_N Mongolia_North_N -0.700
  264. gendstat: Iran_GanjDareh_N Russia_HG_Karelia -0.396
  265. gendstat: Iran_GanjDareh_N Serbia_EN_Starcevo -0.623
  266. gendstat: Satsurblia_HG Mongolia_North_N -0.878
  267. gendstat: Satsurblia_HG Russia_HG_Karelia -0.635
  268. gendstat: Satsurblia_HG Serbia_EN_Starcevo -0.844
  269. gendstat: Mongolia_North_N Russia_HG_Karelia 0.184
  270. gendstat: Mongolia_North_N Serbia_EN_Starcevo -0.080
  271. gendstat: Russia_HG_Karelia Serbia_EN_Starcevo -0.210
  272.  
  273. ##end of qpAdm: 255.234 seconds cpu 1350.361 Mbytes in use
  274.  
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