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comparison test-data/example_harvester_archive/Admix_run_007_f @ 0:8a7390c4d6bf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
author iuc
date Mon, 11 Dec 2017 04:37:17 -0500
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1
2
3 ----------------------------------------------------
4 STRUCTURE by Pritchard, Stephens and Donnelly (2000)
5 Code by J.K. Pritchard
6 Modified by Daniel Falush to
7 incorporate recombination breakpoints
8 Version 2.0 (July 2001)
9 ----------------------------------------------------
10
11
12
13 Command line arguments: bin/structure.exe -m \mainparams -e \extraparams
14 Input File: \project_data
15
16 Run parameters:
17 95 individuals
18 18 loci
19 4 populations assumed
20 50000 Burn-in period
21 500000 Reps
22
23
24 --------------------------------------------
25 Proportion of membership of each pre-defined
26 population in each of the 4 clusters
27
28 Given Inferred Clusters Number of
29 Pop 1 2 3 4 Individuals
30
31 1: 0.991 0.003 0.005 0.001 6
32 2: 0.990 0.002 0.006 0.002 6
33 3: 0.995 0.001 0.002 0.001 6
34 4: 0.968 0.003 0.027 0.002 6
35 5: 0.212 0.003 0.783 0.002 6
36 6: 0.104 0.015 0.878 0.003 6
37 7: 0.991 0.002 0.006 0.001 6
38 8: 0.022 0.002 0.974 0.002 6
39 9: 0.003 0.006 0.989 0.001 6
40 10: 0.036 0.021 0.940 0.004 6
41 11: 0.002 0.988 0.009 0.001 6
42 12: 0.002 0.995 0.002 0.001 6
43 13: 0.002 0.994 0.003 0.001 6
44 14: 0.002 0.995 0.002 0.001 6
45 15: 0.001 0.001 0.001 0.997 6
46 16: 0.001 0.002 0.002 0.995 5
47 --------------------------------------------
48
49 Allele-freq. divergence among pops (Kullback-Leibler distance),
50 computed using point estimates of P.
51
52 1 2 3 4
53 1 - 1.82 0.54 2.44
54 2 1.91 - 1.05 2.63
55 3 0.75 1.36 - 2.31
56 4 3.37 3.50 2.55 -
57 --------------------------------------------
58 Estimated Ln Prob of Data = -2773.7
59 Mean value of ln likelihood = -2678.7
60 Variance of ln likelihood = 190.1
61 Mean value of alpha = 0.0270
62
63 Mean value of Fst_1 = 0.2745
64 Mean value of Fst_2 = 0.3296
65 Mean value of Fst_3 = 0.1303
66 Mean value of Fst_4 = 0.5180
67
68
69 Inferred ancestry of individuals:
70 Label (%Miss) Pop: Inferred clusters
71 1 A01 (0) 1 : 0.994 0.002 0.003 0.001
72 2 A02 (0) 1 : 0.995 0.001 0.003 0.001
73 3 A03 (0) 1 : 0.981 0.007 0.010 0.001
74 4 A04 (0) 1 : 0.995 0.002 0.002 0.001
75 5 A05 (0) 1 : 0.994 0.002 0.003 0.001
76 6 A24 (0) 1 : 0.989 0.002 0.008 0.002
77 7 B466 (0) 2 : 0.992 0.002 0.005 0.001
78 8 B479 (0) 2 : 0.995 0.001 0.003 0.001
79 9 B480 (0) 2 : 0.991 0.002 0.006 0.001
80 10 B482 (0) 2 : 0.984 0.003 0.010 0.003
81 11 B484 (0) 2 : 0.985 0.002 0.011 0.002
82 12 B485 (0) 2 : 0.993 0.002 0.004 0.001
83 13 C02 (0) 3 : 0.996 0.001 0.002 0.001
84 14 C05 (0) 3 : 0.995 0.001 0.002 0.001
85 15 C14 (0) 3 : 0.995 0.001 0.002 0.001
86 16 C30 (0) 3 : 0.995 0.002 0.002 0.001
87 17 C31 (0) 3 : 0.995 0.001 0.002 0.001
88 18 C40 (0) 3 : 0.995 0.001 0.003 0.001
89 19 D08 (0) 4 : 0.989 0.001 0.007 0.002
90 20 D09 (0) 4 : 0.990 0.002 0.006 0.001
91 21 D13 (0) 4 : 0.988 0.002 0.008 0.003
92 22 D21 (0) 4 : 0.975 0.007 0.016 0.002
93 23 D25 (0) 4 : 0.984 0.003 0.011 0.001
94 24 D30 (0) 4 : 0.881 0.004 0.114 0.001
95 25 E01 (0) 5 : 0.042 0.002 0.953 0.003
96 26 E02 (0) 5 : 0.009 0.002 0.988 0.002
97 27 E03 (0) 5 : 0.738 0.002 0.257 0.002
98 28 E04 (0) 5 : 0.332 0.002 0.664 0.002
99 29 E05 (0) 5 : 0.113 0.002 0.883 0.001
100 30 E06 (0) 5 : 0.038 0.005 0.956 0.001
101 31 F03 (0) 6 : 0.068 0.003 0.919 0.010
102 32 F05 (0) 6 : 0.040 0.011 0.948 0.001
103 33 F08 (0) 6 : 0.020 0.007 0.970 0.004
104 34 F14 (0) 6 : 0.471 0.065 0.463 0.001
105 35 F25 (0) 6 : 0.015 0.003 0.981 0.001
106 36 F35 (0) 6 : 0.010 0.002 0.987 0.001
107 37 B360 (0) 7 : 0.993 0.002 0.004 0.001
108 38 B365 (0) 7 : 0.993 0.002 0.003 0.001
109 39 B367 (0) 7 : 0.980 0.001 0.018 0.001
110 40 B370 (0) 7 : 0.994 0.002 0.003 0.001
111 41 B371 (0) 7 : 0.994 0.002 0.003 0.001
112 42 B372 (0) 7 : 0.994 0.002 0.003 0.001
113 43 B341 (0) 8 : 0.016 0.004 0.976 0.004
114 44 B342 (0) 8 : 0.065 0.002 0.932 0.001
115 45 B343 (0) 8 : 0.019 0.002 0.978 0.001
116 46 B345 (0) 8 : 0.011 0.002 0.985 0.001
117 47 B346 (0) 8 : 0.008 0.002 0.989 0.001
118 48 B349 (0) 8 : 0.012 0.002 0.985 0.001
119 49 B121 (0) 9 : 0.003 0.004 0.991 0.002
120 50 B122 (0) 9 : 0.002 0.010 0.987 0.001
121 51 B125 (0) 9 : 0.003 0.003 0.993 0.002
122 52 B127 (0) 9 : 0.003 0.003 0.993 0.001
123 53 B128 (0) 9 : 0.004 0.008 0.986 0.002
124 54 B129 (0) 9 : 0.003 0.010 0.985 0.002
125 55 B306 (0) 10 : 0.002 0.002 0.987 0.009
126 56 B310 (0) 10 : 0.002 0.023 0.973 0.001
127 57 B312 (0) 10 : 0.035 0.029 0.934 0.002
128 58 B313 (0) 10 : 0.003 0.017 0.973 0.007
129 59 B317 (0) 10 : 0.165 0.045 0.788 0.001
130 60 B318 (0) 10 : 0.006 0.007 0.985 0.002
131 61 G19 (0) 11 : 0.002 0.995 0.002 0.001
132 62 G20 (0) 11 : 0.002 0.994 0.003 0.001
133 63 G21 (0) 11 : 0.002 0.995 0.002 0.001
134 64 G22 (0) 11 : 0.003 0.959 0.037 0.001
135 65 G23 (0) 11 : 0.002 0.993 0.004 0.001
136 66 G24 (0) 11 : 0.002 0.994 0.003 0.001
137 67 H01 (0) 12 : 0.002 0.995 0.002 0.001
138 68 H02 (0) 12 : 0.001 0.995 0.003 0.001
139 69 H03 (0) 12 : 0.002 0.995 0.002 0.001
140 70 H04 (0) 12 : 0.002 0.995 0.002 0.001
141 71 H05 (0) 12 : 0.002 0.995 0.002 0.001
142 72 H12 (0) 12 : 0.001 0.996 0.002 0.001
143 73 I20 (0) 13 : 0.002 0.996 0.002 0.001
144 74 I21 (0) 13 : 0.002 0.996 0.002 0.001
145 75 I23 (0) 13 : 0.004 0.989 0.004 0.002
146 76 I24 (0) 13 : 0.002 0.995 0.002 0.001
147 77 I25 (0) 13 : 0.001 0.993 0.005 0.001
148 78 I26 (0) 13 : 0.002 0.996 0.002 0.001
149 79 J02 (0) 14 : 0.001 0.996 0.002 0.001
150 80 J04 (0) 14 : 0.002 0.995 0.002 0.001
151 81 J05 (0) 14 : 0.002 0.994 0.003 0.001
152 82 J08 (0) 14 : 0.005 0.991 0.003 0.001
153 83 J09 (0) 14 : 0.002 0.995 0.002 0.001
154 84 J10 (0) 14 : 0.001 0.996 0.001 0.001
155 85 K20 (5) 15 : 0.001 0.001 0.001 0.996
156 86 K33 (5) 15 : 0.001 0.001 0.001 0.997
157 87 K34 (5) 15 : 0.001 0.001 0.001 0.997
158 88 K35 (5) 15 : 0.001 0.001 0.001 0.996
159 89 K53 (5) 15 : 0.001 0.001 0.001 0.997
160 90 K56 (5) 15 : 0.001 0.001 0.001 0.997
161 91 L04 (5) 16 : 0.001 0.001 0.001 0.997
162 92 L07 (5) 16 : 0.001 0.001 0.001 0.997
163 93 L14 (5) 16 : 0.001 0.006 0.004 0.989
164 94 L26 (5) 16 : 0.001 0.001 0.001 0.996
165 95 L27 (5) 16 : 0.001 0.001 0.001 0.996
166
167
168 Estimated Allele Frequencies in each population
169 First column gives estimated ancestral frequencies
170
171
172 Locus 1 : L1
173 7 alleles
174 0.0% missing data
175 118 (0.461) 0.704 0.478 0.807 0.019
176 127 (0.086) 0.186 0.004 0.022 0.004
177 130 (0.110) 0.034 0.005 0.027 0.487
178 114 (0.083) 0.065 0.003 0.023 0.003
179 122 (0.118) 0.005 0.244 0.093 0.005
180 110 (0.085) 0.004 0.265 0.022 0.003
181 135 (0.056) 0.002 0.002 0.006 0.479
182
183 Locus 2 : L2
184 15 alleles
185 0.0% missing data
186 228 (0.071) 0.245 0.003 0.049 0.003
187 222 (0.112) 0.079 0.036 0.278 0.005
188 225 (0.094) 0.286 0.004 0.203 0.004
189 234 (0.056) 0.017 0.002 0.022 0.002
190 219 (0.118) 0.224 0.146 0.112 0.005
191 213 (0.122) 0.118 0.610 0.111 0.005
192 204 (0.041) 0.016 0.002 0.005 0.002
193 216 (0.065) 0.003 0.083 0.039 0.003
194 195 (0.045) 0.002 0.002 0.037 0.002
195 231 (0.049) 0.002 0.002 0.070 0.002
196 210 (0.063) 0.003 0.043 0.039 0.003
197 240 (0.042) 0.002 0.002 0.021 0.002
198 207 (0.043) 0.002 0.061 0.005 0.002
199 198 (0.040) 0.002 0.002 0.004 0.917
200 185 (0.038) 0.002 0.002 0.004 0.044
201
202 Locus 3 : L3
203 3 alleles
204 0.0% missing data
205 266 (0.835) 0.932 0.993 0.968 0.035
206 272 (0.098) 0.066 0.004 0.025 0.004
207 278 (0.067) 0.003 0.003 0.007 0.961
208
209 Locus 4 : L4
210 19 alleles
211 0.0% missing data
212 164 (0.101) 0.127 0.165 0.087 0.004
213 173 (0.104) 0.572 0.004 0.428 0.004
214 182 (0.045) 0.196 0.002 0.005 0.002
215 170 (0.054) 0.016 0.043 0.006 0.002
216 200 (0.045) 0.002 0.002 0.053 0.002
217 202 (0.040) 0.002 0.002 0.020 0.002
218 176 (0.040) 0.002 0.002 0.020 0.002
219 185 (0.042) 0.062 0.002 0.005 0.002
220 167 (0.066) 0.003 0.062 0.072 0.003
221 158 (0.073) 0.003 0.063 0.169 0.003
222 155 (0.062) 0.003 0.045 0.053 0.003
223 152 (0.055) 0.002 0.183 0.020 0.002
224 179 (0.040) 0.002 0.002 0.020 0.002
225 145 (0.041) 0.002 0.002 0.021 0.002
226 149 (0.043) 0.002 0.199 0.005 0.002
227 161 (0.042) 0.002 0.219 0.005 0.002
228 136 (0.038) 0.002 0.002 0.004 0.874
229 101 (0.036) 0.001 0.002 0.004 0.044
230 139 (0.036) 0.001 0.002 0.004 0.044
231
232 Locus 5 : L5
233 24 alleles
234 0.0% missing data
235 182 (0.058) 0.099 0.002 0.063 0.090
236 188 (0.032) 0.092 0.001 0.004 0.001
237 185 (0.043) 0.185 0.002 0.033 0.002
238 194 (0.041) 0.060 0.002 0.022 0.002
239 209 (0.029) 0.016 0.001 0.003 0.001
240 191 (0.044) 0.048 0.002 0.035 0.002
241 160 (0.067) 0.026 0.062 0.045 0.268
242 200 (0.040) 0.047 0.002 0.020 0.002
243 173 (0.049) 0.155 0.002 0.018 0.089
244 176 (0.040) 0.049 0.002 0.018 0.002
245 169 (0.040) 0.012 0.002 0.057 0.002
246 131 (0.029) 0.001 0.001 0.019 0.001
247 166 (0.035) 0.001 0.001 0.100 0.001
248 154 (0.047) 0.002 0.061 0.101 0.002
249 144 (0.050) 0.002 0.206 0.112 0.002
250 157 (0.045) 0.002 0.101 0.053 0.002
251 203 (0.034) 0.004 0.002 0.032 0.001
252 147 (0.047) 0.002 0.060 0.103 0.002
253 134 (0.066) 0.113 0.283 0.078 0.003
254 141 (0.044) 0.077 0.120 0.005 0.002
255 206 (0.033) 0.001 0.001 0.068 0.001
256 151 (0.030) 0.001 0.060 0.003 0.001
257 137 (0.029) 0.001 0.021 0.003 0.001
258 179 (0.028) 0.001 0.001 0.003 0.520
259
260 Locus 6 : L6
261 6 alleles
262 11.6% missing data
263 177 (0.216) 0.300 0.109 0.081 0.225
264 165 (0.225) 0.229 0.028 0.174 0.231
265 171 (0.340) 0.463 0.014 0.721 0.343
266 175 (0.078) 0.003 0.543 0.008 0.072
267 183 (0.071) 0.003 0.163 0.008 0.065
268 179 (0.070) 0.003 0.143 0.008 0.064
269
270 Locus 7 : L7
271 10 alleles
272 0.0% missing data
273 187 (0.178) 0.360 0.007 0.444 0.007
274 191 (0.118) 0.292 0.005 0.092 0.005
275 183 (0.186) 0.022 0.486 0.321 0.008
276 195 (0.066) 0.257 0.003 0.009 0.003
277 199 (0.098) 0.051 0.023 0.025 0.004
278 180 (0.085) 0.004 0.063 0.041 0.004
279 203 (0.087) 0.004 0.103 0.041 0.004
280 206 (0.074) 0.005 0.167 0.016 0.003
281 214 (0.058) 0.002 0.140 0.006 0.002
282 138 (0.051) 0.002 0.002 0.006 0.961
283
284 Locus 8 : L8
285 7 alleles
286 0.0% missing data
287 151 (0.402) 0.745 0.693 0.462 0.017
288 148 (0.105) 0.099 0.024 0.022 0.004
289 145 (0.078) 0.004 0.003 0.021 0.962
290 157 (0.057) 0.003 0.002 0.022 0.002
291 155 (0.122) 0.141 0.005 0.093 0.005
292 135 (0.070) 0.003 0.003 0.073 0.003
293 141 (0.164) 0.007 0.269 0.306 0.007
294
295 Locus 9 : L9
296 10 alleles
297 0.0% missing data
298 138 (0.194) 0.769 0.008 0.295 0.008
299 140 (0.063) 0.092 0.003 0.007 0.003
300 147 (0.140) 0.006 0.006 0.270 0.965
301 142 (0.145) 0.113 0.346 0.043 0.006
302 145 (0.132) 0.006 0.107 0.189 0.005
303 136 (0.073) 0.003 0.003 0.088 0.003
304 134 (0.062) 0.003 0.003 0.039 0.003
305 132 (0.065) 0.003 0.003 0.055 0.003
306 153 (0.066) 0.003 0.420 0.007 0.003
307 149 (0.060) 0.002 0.102 0.007 0.002
308
309 Locus 10 : L10
310 7 alleles
311 0.0% missing data
312 313 (0.082) 0.196 0.003 0.011 0.003
313 317 (0.331) 0.707 0.014 0.659 0.014
314 321 (0.119) 0.035 0.005 0.077 0.005
315 319 (0.170) 0.035 0.007 0.099 0.446
316 325 (0.062) 0.017 0.003 0.007 0.003
317 306 (0.174) 0.007 0.966 0.140 0.007
318 324 (0.063) 0.003 0.003 0.007 0.522
319
320 Locus 11 : L11
321 8 alleles
322 0.0% missing data
323 250 (0.220) 0.486 0.009 0.379 0.009
324 247 (0.070) 0.153 0.003 0.008 0.003
325 242 (0.073) 0.227 0.003 0.009 0.003
326 251 (0.112) 0.040 0.005 0.086 0.005
327 245 (0.200) 0.080 0.108 0.168 0.008
328 257 (0.066) 0.003 0.003 0.039 0.003
329 243 (0.160) 0.007 0.865 0.045 0.965
330 253 (0.099) 0.004 0.004 0.267 0.004
331
332 Locus 12 : L12
333 4 alleles
334 0.0% missing data
335 204 (0.818) 0.963 0.833 0.979 0.950
336 180 (0.062) 0.032 0.003 0.007 0.003
337 218 (0.065) 0.003 0.162 0.007 0.003
338 210 (0.055) 0.002 0.002 0.006 0.045
339
340 Locus 13 : L13
341 6 alleles
342 0.0% missing data
343 260 (0.642) 0.932 0.886 0.843 0.856
344 263 (0.138) 0.029 0.006 0.133 0.093
345 257 (0.056) 0.032 0.002 0.006 0.002
346 269 (0.058) 0.002 0.082 0.006 0.002
347 275 (0.054) 0.002 0.022 0.006 0.002
348 246 (0.051) 0.002 0.002 0.006 0.045
349
350 Locus 14 : L14
351 5 alleles
352 0.0% missing data
353 157 (0.586) 0.947 0.884 0.366 0.983
354 146 (0.182) 0.042 0.008 0.532 0.007
355 153 (0.072) 0.003 0.003 0.055 0.003
356 155 (0.101) 0.005 0.084 0.041 0.004
357 163 (0.059) 0.002 0.022 0.006 0.002
358
359 Locus 15 : L15
360 2 alleles
361 0.0% missing data
362 243 (0.697) 0.985 0.029 0.774 0.950
363 238 (0.303) 0.015 0.971 0.226 0.050
364
365 Locus 16 : L16
366 3 alleles
367 0.0% missing data
368 173 (0.777) 0.901 0.873 0.766 0.991
369 165 (0.068) 0.093 0.003 0.008 0.003
370 169 (0.155) 0.006 0.124 0.227 0.006
371
372 Locus 17 : L17
373 2 alleles
374 0.0% missing data
375 171 (0.931) 0.997 0.997 0.992 0.039
376 168 (0.069) 0.003 0.003 0.008 0.961
377
378 Locus 18 : L18
379 4 alleles
380 0.0% missing data
381 286 (0.738) 0.824 0.970 0.926 0.030
382 287 (0.076) 0.169 0.003 0.008 0.003
383 283 (0.097) 0.004 0.023 0.043 0.004
384 290 (0.089) 0.004 0.004 0.023 0.962
385
386 Values of parameters used in structure:
387 DATAFILE= 34\project_data, OUTFILE= \Results\DAE Admix_run_61, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=4, BURNIN=50000, NUMREPS=500000, USEPOPINFO=0, INFERALPHA=1, INFERLAMBDA=0, POPSPECIFICLAMBDA=0, POPALPHAS=0, COMPUTEPROB=1, NOADMIX=0, ADMBURNIN=2500, UPDATEFREQ=1, PRINTLIKES=0, INTERMEDSAVE=0, PRINTKLD=0, PRINTLAMBDA=0, ANCESTDIST=0, NUMBOXES=1000, ANCESTPINT=0.90000, GENSBACK=2, MIGRPRIOR=0.05000, PRINTQHAT=0, PRINTQSUM=0, ALPHA=1.0000, FREQSCORR=1, FPRIORMEAN=0.0100, FPRIORSD=0.0500, ONEFST=0, LAMBDA=1.0000, UNIFPRIORALPHA=1, ALPHAMAX=10.0000, ALPHAPRIORA=1.0000, ALPHAPRIORB=2.0000, ALPHAPROPSD=0.0250, STARTATPOPINFO=0, RANDOMIZE=1, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0
388 [STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9,