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comparison test-data/example_harvester_archive/Admix_run_002_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 2 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 2 clusters
27
28 Given Inferred Clusters Number of
29 Pop 1 2 Individuals
30
31 1: 0.006 0.994 6
32 2: 0.005 0.995 6
33 3: 0.004 0.996 6
34 4: 0.015 0.985 6
35 5: 0.013 0.987 6
36 6: 0.091 0.909 6
37 7: 0.007 0.993 6
38 8: 0.024 0.976 6
39 9: 0.638 0.362 6
40 10: 0.485 0.515 6
41 11: 0.995 0.005 6
42 12: 0.996 0.004 6
43 13: 0.996 0.004 6
44 14: 0.995 0.005 6
45 15: 0.004 0.996 6
46 16: 0.005 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
53 1 - 1.44
54 2 1.50 -
55 --------------------------------------------
56 Estimated Ln Prob of Data = -3631.9
57 Mean value of ln likelihood = -3562.2
58 Variance of ln likelihood = 139.5
59 Mean value of alpha = 0.0695
60
61 Mean value of Fst_1 = 0.2830
62 Mean value of Fst_2 = 0.1203
63
64
65 Inferred ancestry of individuals:
66 Label (%Miss) Pop: Inferred clusters
67 1 A01 (0) 1 : 0.005 0.995
68 2 A02 (0) 1 : 0.005 0.995
69 3 A03 (0) 1 : 0.009 0.991
70 4 A04 (0) 1 : 0.005 0.995
71 5 A05 (0) 1 : 0.006 0.994
72 6 A24 (0) 1 : 0.005 0.995
73 7 B466 (0) 2 : 0.005 0.995
74 8 B479 (0) 2 : 0.005 0.995
75 9 B480 (0) 2 : 0.005 0.995
76 10 B482 (0) 2 : 0.006 0.994
77 11 B484 (0) 2 : 0.004 0.996
78 12 B485 (0) 2 : 0.006 0.994
79 13 C02 (0) 3 : 0.004 0.996
80 14 C05 (0) 3 : 0.004 0.996
81 15 C14 (0) 3 : 0.004 0.996
82 16 C30 (0) 3 : 0.005 0.995
83 17 C31 (0) 3 : 0.004 0.996
84 18 C40 (0) 3 : 0.004 0.996
85 19 D08 (0) 4 : 0.004 0.996
86 20 D09 (0) 4 : 0.011 0.989
87 21 D13 (0) 4 : 0.007 0.993
88 22 D21 (0) 4 : 0.016 0.984
89 23 D25 (0) 4 : 0.014 0.986
90 24 D30 (0) 4 : 0.037 0.963
91 25 E01 (0) 5 : 0.017 0.983
92 26 E02 (0) 5 : 0.019 0.981
93 27 E03 (0) 5 : 0.006 0.994
94 28 E04 (0) 5 : 0.009 0.991
95 29 E05 (0) 5 : 0.006 0.994
96 30 E06 (0) 5 : 0.019 0.981
97 31 F03 (0) 6 : 0.009 0.991
98 32 F05 (0) 6 : 0.185 0.815
99 33 F08 (0) 6 : 0.095 0.905
100 34 F14 (0) 6 : 0.155 0.845
101 35 F25 (0) 6 : 0.023 0.977
102 36 F35 (0) 6 : 0.081 0.919
103 37 B360 (0) 7 : 0.006 0.994
104 38 B365 (0) 7 : 0.010 0.990
105 39 B367 (0) 7 : 0.005 0.995
106 40 B370 (0) 7 : 0.007 0.993
107 41 B371 (0) 7 : 0.008 0.992
108 42 B372 (0) 7 : 0.007 0.993
109 43 B341 (0) 8 : 0.008 0.992
110 44 B342 (0) 8 : 0.019 0.981
111 45 B343 (0) 8 : 0.014 0.986
112 46 B345 (0) 8 : 0.075 0.925
113 47 B346 (0) 8 : 0.009 0.991
114 48 B349 (0) 8 : 0.019 0.981
115 49 B121 (0) 9 : 0.439 0.561
116 50 B122 (0) 9 : 0.885 0.115
117 51 B125 (0) 9 : 0.452 0.548
118 52 B127 (0) 9 : 0.751 0.249
119 53 B128 (0) 9 : 0.651 0.349
120 54 B129 (0) 9 : 0.650 0.350
121 55 B306 (0) 10 : 0.407 0.593
122 56 B310 (0) 10 : 0.554 0.446
123 57 B312 (0) 10 : 0.542 0.458
124 58 B313 (0) 10 : 0.541 0.459
125 59 B317 (0) 10 : 0.427 0.573
126 60 B318 (0) 10 : 0.435 0.565
127 61 G19 (0) 11 : 0.996 0.004
128 62 G20 (0) 11 : 0.995 0.005
129 63 G21 (0) 11 : 0.996 0.004
130 64 G22 (0) 11 : 0.993 0.007
131 65 G23 (0) 11 : 0.995 0.005
132 66 G24 (0) 11 : 0.995 0.005
133 67 H01 (0) 12 : 0.995 0.005
134 68 H02 (0) 12 : 0.996 0.004
135 69 H03 (0) 12 : 0.996 0.004
136 70 H04 (0) 12 : 0.996 0.004
137 71 H05 (0) 12 : 0.996 0.004
138 72 H12 (0) 12 : 0.997 0.003
139 73 I20 (0) 13 : 0.996 0.004
140 74 I21 (0) 13 : 0.996 0.004
141 75 I23 (0) 13 : 0.994 0.006
142 76 I24 (0) 13 : 0.996 0.004
143 77 I25 (0) 13 : 0.996 0.004
144 78 I26 (0) 13 : 0.996 0.004
145 79 J02 (0) 14 : 0.996 0.004
146 80 J04 (0) 14 : 0.995 0.005
147 81 J05 (0) 14 : 0.995 0.005
148 82 J08 (0) 14 : 0.992 0.008
149 83 J09 (0) 14 : 0.996 0.004
150 84 J10 (0) 14 : 0.997 0.003
151 85 K20 (5) 15 : 0.004 0.996
152 86 K33 (5) 15 : 0.004 0.996
153 87 K34 (5) 15 : 0.004 0.996
154 88 K35 (5) 15 : 0.004 0.996
155 89 K53 (5) 15 : 0.004 0.996
156 90 K56 (5) 15 : 0.004 0.996
157 91 L04 (5) 16 : 0.004 0.996
158 92 L07 (5) 16 : 0.004 0.996
159 93 L14 (5) 16 : 0.007 0.993
160 94 L26 (5) 16 : 0.004 0.996
161 95 L27 (5) 16 : 0.004 0.996
162
163
164 Estimated Allele Frequencies in each population
165 First column gives estimated ancestral frequencies
166
167
168 Locus 1 : L1
169 7 alleles
170 0.0% missing data
171 118 (0.436) 0.552 0.626
172 127 (0.098) 0.004 0.103
173 130 (0.102) 0.004 0.110
174 114 (0.077) 0.003 0.042
175 122 (0.123) 0.219 0.028
176 110 (0.069) 0.214 0.004
177 135 (0.094) 0.004 0.087
178
179 Locus 2 : L2
180 15 alleles
181 0.0% missing data
182 228 (0.071) 0.004 0.146
183 222 (0.114) 0.076 0.142
184 225 (0.082) 0.004 0.236
185 234 (0.048) 0.002 0.017
186 219 (0.118) 0.118 0.160
187 213 (0.112) 0.548 0.065
188 204 (0.042) 0.002 0.010
189 216 (0.073) 0.065 0.018
190 195 (0.047) 0.002 0.017
191 231 (0.046) 0.059 0.004
192 210 (0.048) 0.060 0.004
193 240 (0.042) 0.008 0.006
194 207 (0.044) 0.047 0.002
195 198 (0.073) 0.003 0.161
196 185 (0.042) 0.002 0.010
197
198 Locus 3 : L3
199 3 alleles
200 0.0% missing data
201 266 (0.766) 0.991 0.784
202 272 (0.090) 0.004 0.042
203 278 (0.144) 0.006 0.174
204
205 Locus 4 : L4
206 19 alleles
207 0.0% missing data
208 164 (0.100) 0.155 0.085
209 173 (0.091) 0.003 0.505
210 182 (0.061) 0.002 0.105
211 170 (0.061) 0.031 0.011
212 200 (0.048) 0.002 0.026
213 202 (0.040) 0.003 0.009
214 176 (0.041) 0.002 0.010
215 185 (0.050) 0.002 0.034
216 167 (0.046) 0.097 0.004
217 158 (0.051) 0.178 0.005
218 155 (0.045) 0.069 0.004
219 152 (0.045) 0.140 0.003
220 179 (0.040) 0.008 0.007
221 145 (0.040) 0.006 0.008
222 149 (0.045) 0.141 0.003
223 161 (0.045) 0.155 0.003
224 136 (0.068) 0.002 0.160
225 101 (0.040) 0.002 0.010
226 139 (0.041) 0.002 0.010
227
228 Locus 5 : L5
229 24 alleles
230 0.0% missing data
231 182 (0.041) 0.002 0.097
232 188 (0.038) 0.001 0.049
233 185 (0.041) 0.002 0.113
234 194 (0.037) 0.001 0.042
235 209 (0.030) 0.001 0.010
236 191 (0.038) 0.001 0.042
237 160 (0.061) 0.043 0.082
238 200 (0.036) 0.001 0.034
239 173 (0.042) 0.002 0.105
240 176 (0.037) 0.002 0.033
241 169 (0.043) 0.034 0.015
242 131 (0.030) 0.001 0.010
243 166 (0.037) 0.001 0.049
244 154 (0.056) 0.054 0.044
245 144 (0.046) 0.212 0.015
246 157 (0.050) 0.081 0.020
247 203 (0.035) 0.006 0.015
248 147 (0.042) 0.113 0.009
249 134 (0.065) 0.248 0.068
250 141 (0.058) 0.085 0.042
251 206 (0.034) 0.050 0.005
252 151 (0.031) 0.042 0.002
253 137 (0.030) 0.015 0.002
254 179 (0.041) 0.001 0.097
255
256 Locus 6 : L6
257 6 alleles
258 11.6% missing data
259 177 (0.234) 0.104 0.202
260 165 (0.202) 0.052 0.198
261 171 (0.337) 0.089 0.586
262 175 (0.082) 0.482 0.005
263 183 (0.073) 0.145 0.004
264 179 (0.072) 0.127 0.004
265
266 Locus 7 : L7
267 10 alleles
268 0.0% missing data
269 187 (0.145) 0.012 0.372
270 191 (0.106) 0.005 0.182
271 183 (0.160) 0.556 0.074
272 195 (0.094) 0.004 0.130
273 199 (0.095) 0.019 0.035
274 180 (0.091) 0.053 0.019
275 203 (0.081) 0.096 0.012
276 206 (0.069) 0.139 0.006
277 214 (0.058) 0.112 0.003
278 138 (0.101) 0.004 0.167
279
280 Locus 8 : L8
281 7 alleles
282 0.0% missing data
283 151 (0.437) 0.502 0.605
284 148 (0.121) 0.020 0.061
285 145 (0.122) 0.004 0.188
286 157 (0.056) 0.004 0.010
287 155 (0.105) 0.004 0.116
288 135 (0.075) 0.043 0.012
289 141 (0.084) 0.423 0.007
290
291 Locus 9 : L9
292 10 alleles
293 0.0% missing data
294 138 (0.172) 0.011 0.496
295 140 (0.076) 0.003 0.047
296 147 (0.150) 0.019 0.275
297 142 (0.155) 0.291 0.071
298 145 (0.124) 0.200 0.037
299 136 (0.072) 0.003 0.040
300 134 (0.060) 0.003 0.017
301 132 (0.066) 0.036 0.010
302 153 (0.067) 0.350 0.004
303 149 (0.059) 0.085 0.003
304
305 Locus 10 : L10
306 7 alleles
307 0.0% missing data
308 313 (0.122) 0.005 0.100
309 317 (0.357) 0.047 0.617
310 321 (0.098) 0.005 0.048
311 319 (0.146) 0.013 0.127
312 325 (0.064) 0.003 0.011
313 306 (0.096) 0.921 0.005
314 324 (0.118) 0.005 0.093
315
316 Locus 11 : L11
317 8 alleles
318 0.0% missing data
319 250 (0.164) 0.008 0.418
320 247 (0.090) 0.003 0.081
321 242 (0.100) 0.004 0.120
322 251 (0.092) 0.013 0.053
323 245 (0.162) 0.087 0.112
324 257 (0.063) 0.003 0.019
325 243 (0.249) 0.655 0.188
326 253 (0.080) 0.228 0.009
327
328 Locus 12 : L12
329 4 alleles
330 0.0% missing data
331 204 (0.795) 0.869 0.966
332 180 (0.070) 0.003 0.019
333 218 (0.073) 0.126 0.004
334 210 (0.061) 0.002 0.011
335
336 Locus 13 : L13
337 6 alleles
338 0.0% missing data
339 260 (0.654) 0.910 0.876
340 263 (0.100) 0.004 0.088
341 257 (0.066) 0.003 0.019
342 269 (0.064) 0.063 0.004
343 275 (0.058) 0.017 0.003
344 246 (0.058) 0.002 0.011
345
346 Locus 14 : L14
347 5 alleles
348 0.0% missing data
349 157 (0.592) 0.892 0.692
350 146 (0.170) 0.015 0.260
351 153 (0.073) 0.003 0.026
352 155 (0.107) 0.071 0.019
353 163 (0.058) 0.018 0.003
354
355 Locus 15 : L15
356 2 alleles
357 0.0% missing data
358 243 (0.690) 0.101 0.918
359 238 (0.310) 0.899 0.082
360
361 Locus 16 : L16
362 3 alleles
363 0.0% missing data
364 173 (0.737) 0.805 0.891
365 165 (0.090) 0.004 0.050
366 169 (0.173) 0.191 0.059
367
368 Locus 17 : L17
369 2 alleles
370 0.0% missing data
371 171 (0.850) 0.994 0.826
372 168 (0.150) 0.006 0.174
373
374 Locus 18 : L18
375 4 alleles
376 0.0% missing data
377 286 (0.676) 0.949 0.722
378 287 (0.108) 0.004 0.089
379 283 (0.076) 0.042 0.007
380 290 (0.140) 0.006 0.182
381
382 Values of parameters used in structure:
383 DATAFILE=\project_data, OUTFILE=\Results_run_3, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=2, 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
384 [STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9,