Mercurial > repos > iuc > structureharvester

comparison test-data/example_harvester_archive/Admix_run_001_f @ 0:8a7390c4d6bf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:8a7390c4d6bf
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: 0.001 0.999 6
32 2: 0.002 0.998 6
33 3: 0.001 0.999 6
34 4: 0.002 0.998 6
35 5: 0.002 0.998 6
36 6: 0.003 0.997 6
37 7: 0.001 0.999 6
38 8: 0.001 0.999 6
39 9: 0.002 0.998 6
40 10: 0.005 0.995 6
41 11: 0.001 0.999 6
42 12: 0.002 0.998 6
43 13: 0.002 0.998 6
44 14: 0.002 0.998 6
45 15: 0.999 0.001 6
46 16: 0.998 0.002 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 - 2.67
54 2 2.10 -
55 --------------------------------------------
56 Estimated Ln Prob of Data = -3646.5
57 Mean value of ln likelihood = -3597.1
58 Variance of ln likelihood = 98.8
59 Mean value of alpha = 0.0254
60
61 Mean value of Fst_1 = 0.5120
62 Mean value of Fst_2 = 0.0523
63
64
65 Inferred ancestry of individuals:
66 Label (%Miss) Pop: Inferred clusters
67 1 A01 (0) 1 : 0.001 0.999
68 2 A02 (0) 1 : 0.002 0.998
69 3 A03 (0) 1 : 0.001 0.999
70 4 A04 (0) 1 : 0.001 0.999
71 5 A05 (0) 1 : 0.002 0.998
72 6 A24 (0) 1 : 0.001 0.999
73 7 B466 (0) 2 : 0.001 0.999
74 8 B479 (0) 2 : 0.001 0.999
75 9 B480 (0) 2 : 0.001 0.999
76 10 B482 (0) 2 : 0.002 0.998
77 11 B484 (0) 2 : 0.003 0.997
78 12 B485 (0) 2 : 0.001 0.999
79 13 C02 (0) 3 : 0.001 0.999
80 14 C05 (0) 3 : 0.001 0.999
81 15 C14 (0) 3 : 0.001 0.999
82 16 C30 (0) 3 : 0.001 0.999
83 17 C31 (0) 3 : 0.001 0.999
84 18 C40 (0) 3 : 0.001 0.999
85 19 D08 (0) 4 : 0.002 0.998
86 20 D09 (0) 4 : 0.001 0.999
87 21 D13 (0) 4 : 0.003 0.997
88 22 D21 (0) 4 : 0.002 0.998
89 23 D25 (0) 4 : 0.001 0.999
90 24 D30 (0) 4 : 0.001 0.999
91 25 E01 (0) 5 : 0.003 0.997
92 26 E02 (0) 5 : 0.003 0.997
93 27 E03 (0) 5 : 0.001 0.999
94 28 E04 (0) 5 : 0.002 0.998
95 29 E05 (0) 5 : 0.002 0.998
96 30 E06 (0) 5 : 0.002 0.998
97 31 F03 (0) 6 : 0.010 0.990
98 32 F05 (0) 6 : 0.001 0.999
99 33 F08 (0) 6 : 0.002 0.998
100 34 F14 (0) 6 : 0.001 0.999
101 35 F25 (0) 6 : 0.001 0.999
102 36 F35 (0) 6 : 0.001 0.999
103 37 B360 (0) 7 : 0.001 0.999
104 38 B365 (0) 7 : 0.001 0.999
105 39 B367 (0) 7 : 0.001 0.999
106 40 B370 (0) 7 : 0.001 0.999
107 41 B371 (0) 7 : 0.001 0.999
108 42 B372 (0) 7 : 0.001 0.999
109 43 B341 (0) 8 : 0.002 0.998
110 44 B342 (0) 8 : 0.001 0.999
111 45 B343 (0) 8 : 0.001 0.999
112 46 B345 (0) 8 : 0.001 0.999
113 47 B346 (0) 8 : 0.001 0.999
114 48 B349 (0) 8 : 0.001 0.999
115 49 B121 (0) 9 : 0.002 0.998
116 50 B122 (0) 9 : 0.001 0.999
117 51 B125 (0) 9 : 0.003 0.997
118 52 B127 (0) 9 : 0.001 0.999
119 53 B128 (0) 9 : 0.002 0.998
120 54 B129 (0) 9 : 0.003 0.997
121 55 B306 (0) 10 : 0.016 0.984
122 56 B310 (0) 10 : 0.001 0.999
123 57 B312 (0) 10 : 0.002 0.998
124 58 B313 (0) 10 : 0.004 0.996
125 59 B317 (0) 10 : 0.001 0.999
126 60 B318 (0) 10 : 0.005 0.995
127 61 G19 (0) 11 : 0.001 0.999
128 62 G20 (0) 11 : 0.001 0.999
129 63 G21 (0) 11 : 0.001 0.999
130 64 G22 (0) 11 : 0.001 0.999
131 65 G23 (0) 11 : 0.002 0.998
132 66 G24 (0) 11 : 0.001 0.999
133 67 H01 (0) 12 : 0.001 0.999
134 68 H02 (0) 12 : 0.002 0.998
135 69 H03 (0) 12 : 0.001 0.999
136 70 H04 (0) 12 : 0.002 0.998
137 71 H05 (0) 12 : 0.002 0.998
138 72 H12 (0) 12 : 0.002 0.998
139 73 I20 (0) 13 : 0.002 0.998
140 74 I21 (0) 13 : 0.001 0.999
141 75 I23 (0) 13 : 0.002 0.998
142 76 I24 (0) 13 : 0.002 0.998
143 77 I25 (0) 13 : 0.002 0.998
144 78 I26 (0) 13 : 0.002 0.998
145 79 J02 (0) 14 : 0.002 0.998
146 80 J04 (0) 14 : 0.001 0.999
147 81 J05 (0) 14 : 0.001 0.999
148 82 J08 (0) 14 : 0.001 0.999
149 83 J09 (0) 14 : 0.002 0.998
150 84 J10 (0) 14 : 0.001 0.999
151 85 K20 (5) 15 : 0.999 0.001
152 86 K33 (5) 15 : 0.999 0.001
153 87 K34 (5) 15 : 0.999 0.001
154 88 K35 (5) 15 : 0.999 0.001
155 89 K53 (5) 15 : 0.999 0.001
156 90 K56 (5) 15 : 0.999 0.001
157 91 L04 (5) 16 : 0.999 0.001
158 92 L07 (5) 16 : 0.999 0.001
159 93 L14 (5) 16 : 0.996 0.004
160 94 L26 (5) 16 : 0.999 0.001
161 95 L27 (5) 16 : 0.999 0.001
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 (0.478) 0.020 0.670
172 127 (0.104) 0.004 0.080
173 130 (0.081) 0.484 0.024
174 114 (0.069) 0.003 0.034
175 122 (0.119) 0.005 0.103
176 110 (0.107) 0.005 0.086
177 135 (0.042) 0.478 0.004
178
179 Locus 2 : L2
180 15 alleles
181 0.0% missing data
182 228 (0.091) 0.004 0.111
183 222 (0.099) 0.004 0.133
184 225 (0.119) 0.005 0.178
185 234 (0.043) 0.002 0.015
186 219 (0.111) 0.005 0.161
187 213 (0.147) 0.006 0.250
188 204 (0.037) 0.002 0.009
189 216 (0.058) 0.002 0.038
190 195 (0.042) 0.002 0.015
191 231 (0.052) 0.002 0.027
192 210 (0.051) 0.002 0.027
193 240 (0.037) 0.002 0.009
194 207 (0.047) 0.002 0.021
195 198 (0.034) 0.915 0.003
196 185 (0.033) 0.045 0.003
197
198 Locus 3 : L3
199 3 alleles
200 0.0% missing data
201 266 (0.873) 0.037 0.961
202 272 (0.079) 0.003 0.035
203 278 (0.048) 0.959 0.005
204
205 Locus 4 : L4
206 19 alleles
207 0.0% missing data
208 164 (0.081) 0.003 0.121
209 173 (0.146) 0.006 0.357
210 182 (0.066) 0.003 0.076
211 170 (0.043) 0.002 0.020
212 200 (0.043) 0.002 0.020
213 202 (0.034) 0.001 0.009
214 176 (0.033) 0.001 0.009
215 185 (0.045) 0.002 0.026
216 167 (0.054) 0.002 0.043
217 158 (0.067) 0.003 0.076
218 155 (0.049) 0.002 0.032
219 152 (0.061) 0.003 0.060
220 179 (0.033) 0.001 0.009
221 145 (0.034) 0.001 0.009
222 149 (0.061) 0.003 0.060
223 161 (0.063) 0.003 0.065
224 136 (0.031) 0.872 0.003
225 101 (0.029) 0.044 0.003
226 139 (0.029) 0.044 0.003
227
228 Locus 5 : L5
229 24 alleles
230 0.0% missing data
231 182 (0.060) 0.090 0.059
232 188 (0.040) 0.002 0.036
233 185 (0.052) 0.002 0.080
234 194 (0.038) 0.002 0.031
235 209 (0.028) 0.001 0.008
236 191 (0.038) 0.002 0.031
237 160 (0.055) 0.265 0.043
238 200 (0.036) 0.002 0.025
239 173 (0.061) 0.090 0.065
240 176 (0.036) 0.002 0.025
241 169 (0.036) 0.002 0.025
242 131 (0.028) 0.001 0.008
243 166 (0.040) 0.002 0.036
244 154 (0.045) 0.002 0.053
245 144 (0.054) 0.002 0.097
246 157 (0.044) 0.002 0.047
247 203 (0.032) 0.001 0.014
248 147 (0.044) 0.002 0.053
249 134 (0.063) 0.003 0.146
250 141 (0.047) 0.002 0.064
251 206 (0.036) 0.002 0.025
252 151 (0.035) 0.001 0.020
253 137 (0.028) 0.001 0.008
254 179 (0.024) 0.520 0.002
255
256 Locus 6 : L6
257 6 alleles
258 11.6% missing data
259 177 (0.168) 0.166 0.167
260 165 (0.156) 0.152 0.150
261 171 (0.346) 0.358 0.426
262 175 (0.165) 0.160 0.161
263 183 (0.086) 0.086 0.051
264 179 (0.080) 0.078 0.045
265
266 Locus 7 : L7
267 10 alleles
268 0.0% missing data
269 187 (0.202) 0.009 0.288
270 191 (0.125) 0.005 0.141
271 183 (0.185) 0.008 0.254
272 195 (0.105) 0.004 0.102
273 199 (0.063) 0.003 0.033
274 180 (0.063) 0.003 0.033
275 203 (0.071) 0.003 0.045
276 206 (0.078) 0.003 0.056
277 214 (0.070) 0.003 0.044
278 138 (0.039) 0.959 0.004
279
280 Locus 8 : L8
281 7 alleles
282 0.0% missing data
283 151 (0.466) 0.020 0.632
284 148 (0.084) 0.003 0.051
285 145 (0.059) 0.960 0.010
286 157 (0.044) 0.002 0.010
287 155 (0.109) 0.005 0.086
288 135 (0.064) 0.003 0.028
289 141 (0.174) 0.007 0.184
290
291 Locus 9 : L9
292 10 alleles
293 0.0% missing data
294 138 (0.241) 0.010 0.389
295 140 (0.065) 0.003 0.039
296 147 (0.137) 0.964 0.098
297 142 (0.126) 0.005 0.152
298 145 (0.098) 0.004 0.096
299 136 (0.061) 0.003 0.033
300 134 (0.047) 0.002 0.015
301 132 (0.052) 0.002 0.021
302 153 (0.112) 0.005 0.124
303 149 (0.061) 0.003 0.033
304
305 Locus 10 : L10
306 7 alleles
307 0.0% missing data
308 313 (0.102) 0.004 0.080
309 317 (0.368) 0.016 0.493
310 321 (0.073) 0.003 0.039
311 319 (0.109) 0.445 0.047
312 325 (0.044) 0.002 0.010
313 306 (0.262) 0.011 0.327
314 324 (0.042) 0.519 0.004
315
316 Locus 11 : L11
317 8 alleles
318 0.0% missing data
319 250 (0.219) 0.009 0.312
320 247 (0.083) 0.003 0.062
321 242 (0.100) 0.004 0.090
322 251 (0.072) 0.003 0.045
323 245 (0.113) 0.005 0.113
324 257 (0.049) 0.002 0.016
325 243 (0.262) 0.969 0.266
326 253 (0.104) 0.004 0.096
327
328 Locus 12 : L12
329 4 alleles
330 0.0% missing data
331 204 (0.823) 0.950 0.929
332 180 (0.053) 0.002 0.016
333 218 (0.085) 0.004 0.051
334 210 (0.040) 0.044 0.004
335
336 Locus 13 : L13
337 6 alleles
338 0.0% missing data
339 260 (0.696) 0.857 0.884
340 263 (0.111) 0.092 0.059
341 257 (0.050) 0.002 0.016
342 269 (0.061) 0.003 0.028
343 275 (0.043) 0.002 0.010
344 246 (0.038) 0.044 0.004
345
346 Locus 14 : L14
347 5 alleles
348 0.0% missing data
349 157 (0.640) 0.985 0.723
350 146 (0.187) 0.008 0.206
351 153 (0.057) 0.002 0.022
352 155 (0.073) 0.003 0.039
353 163 (0.043) 0.002 0.010
354
355 Locus 15 : L15
356 2 alleles
357 0.0% missing data
358 243 (0.639) 0.943 0.636
359 238 (0.361) 0.057 0.364
360
361 Locus 16 : L16
362 3 alleles
363 0.0% missing data
364 173 (0.788) 0.991 0.845
365 165 (0.077) 0.003 0.040
366 169 (0.135) 0.006 0.115
367
368 Locus 17 : L17
369 2 alleles
370 0.0% missing data
371 171 (0.951) 0.041 0.995
372 168 (0.049) 0.959 0.005
373
374 Locus 18 : L18
375 4 alleles
376 0.0% missing data
377 286 (0.764) 0.032 0.898
378 287 (0.108) 0.005 0.070
379 283 (0.064) 0.003 0.022
380 290 (0.064) 0.960 0.010
381
382 Values of parameters used in structure:
383 DATAFILE=\project_data, OUTFILE=\Results_run_2, 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,