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comparison test-data/example_harvester_archive/Admix_run_005_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 3 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 3 clusters
27
28 Given Inferred Clusters Number of
29 Pop 1 2 3 Individuals
30
31 1: 0.001 0.997 0.002 6
32 2: 0.002 0.997 0.002 6
33 3: 0.001 0.997 0.002 6
34 4: 0.001 0.996 0.003 6
35 5: 0.002 0.995 0.003 6
36 6: 0.003 0.981 0.016 6
37 7: 0.001 0.996 0.002 6
38 8: 0.002 0.994 0.004 6
39 9: 0.002 0.960 0.038 6
40 10: 0.005 0.913 0.081 6
41 11: 0.001 0.004 0.995 6
42 12: 0.001 0.002 0.997 6
43 13: 0.001 0.002 0.996 6
44 14: 0.001 0.002 0.997 6
45 15: 0.998 0.001 0.001 6
46 16: 0.997 0.001 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 3
53 1 - 2.90 3.44
54 2 2.33 - 1.55
55 3 2.61 1.29 -
56 --------------------------------------------
57 Estimated Ln Prob of Data = -3020.8
58 Mean value of ln likelihood = -2945.9
59 Variance of ln likelihood = 149.7
60 Mean value of alpha = 0.0269
61
62 Mean value of Fst_1 = 0.5216
63 Mean value of Fst_2 = 0.1326
64 Mean value of Fst_3 = 0.3273
65
66
67 Inferred ancestry of individuals:
68 Label (%Miss) Pop: Inferred clusters
69 1 A01 (0) 1 : 0.001 0.997 0.002
70 2 A02 (0) 1 : 0.002 0.997 0.002
71 3 A03 (0) 1 : 0.001 0.997 0.002
72 4 A04 (0) 1 : 0.001 0.997 0.002
73 5 A05 (0) 1 : 0.001 0.996 0.002
74 6 A24 (0) 1 : 0.001 0.997 0.002
75 7 B466 (0) 2 : 0.001 0.997 0.002
76 8 B479 (0) 2 : 0.001 0.997 0.002
77 9 B480 (0) 2 : 0.001 0.997 0.002
78 10 B482 (0) 2 : 0.002 0.996 0.002
79 11 B484 (0) 2 : 0.002 0.996 0.002
80 12 B485 (0) 2 : 0.001 0.997 0.002
81 13 C02 (0) 3 : 0.001 0.997 0.001
82 14 C05 (0) 3 : 0.001 0.997 0.001
83 15 C14 (0) 3 : 0.002 0.997 0.001
84 16 C30 (0) 3 : 0.001 0.997 0.002
85 17 C31 (0) 3 : 0.001 0.997 0.002
86 18 C40 (0) 3 : 0.001 0.997 0.002
87 19 D08 (0) 4 : 0.001 0.997 0.001
88 20 D09 (0) 4 : 0.001 0.996 0.003
89 21 D13 (0) 4 : 0.002 0.996 0.002
90 22 D21 (0) 4 : 0.002 0.993 0.005
91 23 D25 (0) 4 : 0.001 0.996 0.003
92 24 D30 (0) 4 : 0.001 0.995 0.003
93 25 E01 (0) 5 : 0.002 0.994 0.004
94 26 E02 (0) 5 : 0.002 0.994 0.004
95 27 E03 (0) 5 : 0.002 0.996 0.002
96 28 E04 (0) 5 : 0.001 0.996 0.002
97 29 E05 (0) 5 : 0.002 0.996 0.002
98 30 E06 (0) 5 : 0.001 0.994 0.004
99 31 F03 (0) 6 : 0.012 0.985 0.003
100 32 F05 (0) 6 : 0.001 0.967 0.032
101 33 F08 (0) 6 : 0.002 0.982 0.015
102 34 F14 (0) 6 : 0.001 0.963 0.036
103 35 F25 (0) 6 : 0.001 0.994 0.005
104 36 F35 (0) 6 : 0.001 0.995 0.003
105 37 B360 (0) 7 : 0.001 0.997 0.002
106 38 B365 (0) 7 : 0.001 0.995 0.003
107 39 B367 (0) 7 : 0.001 0.997 0.002
108 40 B370 (0) 7 : 0.001 0.996 0.003
109 41 B371 (0) 7 : 0.001 0.996 0.002
110 42 B372 (0) 7 : 0.001 0.997 0.002
111 43 B341 (0) 8 : 0.008 0.984 0.008
112 44 B342 (0) 8 : 0.001 0.995 0.004
113 45 B343 (0) 8 : 0.001 0.996 0.002
114 46 B345 (0) 8 : 0.001 0.995 0.004
115 47 B346 (0) 8 : 0.001 0.997 0.002
116 48 B349 (0) 8 : 0.001 0.997 0.002
117 49 B121 (0) 9 : 0.002 0.991 0.007
118 50 B122 (0) 9 : 0.001 0.878 0.120
119 51 B125 (0) 9 : 0.002 0.993 0.005
120 52 B127 (0) 9 : 0.001 0.992 0.007
121 53 B128 (0) 9 : 0.002 0.972 0.026
122 54 B129 (0) 9 : 0.003 0.934 0.064
123 55 B306 (0) 10 : 0.015 0.974 0.010
124 56 B310 (0) 10 : 0.001 0.900 0.099
125 57 B312 (0) 10 : 0.002 0.823 0.175
126 58 B313 (0) 10 : 0.009 0.860 0.131
127 59 B317 (0) 10 : 0.001 0.943 0.055
128 60 B318 (0) 10 : 0.004 0.978 0.018
129 61 G19 (0) 11 : 0.001 0.002 0.997
130 62 G20 (0) 11 : 0.001 0.002 0.997
131 63 G21 (0) 11 : 0.001 0.002 0.997
132 64 G22 (0) 11 : 0.001 0.014 0.985
133 65 G23 (0) 11 : 0.001 0.003 0.996
134 66 G24 (0) 11 : 0.001 0.002 0.997
135 67 H01 (0) 12 : 0.001 0.002 0.997
136 68 H02 (0) 12 : 0.001 0.002 0.997
137 69 H03 (0) 12 : 0.001 0.002 0.997
138 70 H04 (0) 12 : 0.001 0.002 0.997
139 71 H05 (0) 12 : 0.001 0.002 0.997
140 72 H12 (0) 12 : 0.001 0.001 0.997
141 73 I20 (0) 13 : 0.001 0.002 0.997
142 74 I21 (0) 13 : 0.001 0.002 0.997
143 75 I23 (0) 13 : 0.002 0.004 0.993
144 76 I24 (0) 13 : 0.001 0.002 0.997
145 77 I25 (0) 13 : 0.001 0.002 0.997
146 78 I26 (0) 13 : 0.001 0.002 0.997
147 79 J02 (0) 14 : 0.001 0.002 0.997
148 80 J04 (0) 14 : 0.001 0.002 0.997
149 81 J05 (0) 14 : 0.001 0.002 0.997
150 82 J08 (0) 14 : 0.001 0.004 0.995
151 83 J09 (0) 14 : 0.001 0.002 0.997
152 84 J10 (0) 14 : 0.001 0.001 0.997
153 85 K20 (5) 15 : 0.998 0.001 0.001
154 86 K33 (5) 15 : 0.998 0.001 0.001
155 87 K34 (5) 15 : 0.998 0.001 0.001
156 88 K35 (5) 15 : 0.998 0.001 0.001
157 89 K53 (5) 15 : 0.998 0.001 0.001
158 90 K56 (5) 15 : 0.998 0.001 0.001
159 91 L04 (5) 16 : 0.998 0.001 0.001
160 92 L07 (5) 16 : 0.998 0.001 0.001
161 93 L14 (5) 16 : 0.993 0.002 0.005
162 94 L26 (5) 16 : 0.998 0.001 0.001
163 95 L27 (5) 16 : 0.998 0.001 0.001
164
165
166 Estimated Allele Frequencies in each population
167 First column gives estimated ancestral frequencies
168
169
170 Locus 1 : L1
171 7 alleles
172 0.0% missing data
173 118 (0.406) 0.017 0.761 0.476
174 127 (0.106) 0.004 0.110 0.004
175 130 (0.114) 0.486 0.029 0.005
176 114 (0.084) 0.003 0.045 0.003
177 122 (0.141) 0.006 0.045 0.243
178 110 (0.085) 0.003 0.007 0.266
179 135 (0.064) 0.481 0.003 0.003
180
181 Locus 2 : L2
182 15 alleles
183 0.0% missing data
184 228 (0.071) 0.003 0.156 0.003
185 222 (0.101) 0.004 0.174 0.041
186 225 (0.077) 0.003 0.252 0.003
187 234 (0.050) 0.002 0.019 0.002
188 219 (0.112) 0.005 0.173 0.142
189 213 (0.112) 0.005 0.109 0.604
190 204 (0.047) 0.002 0.010 0.002
191 216 (0.074) 0.003 0.020 0.081
192 195 (0.051) 0.002 0.019 0.002
193 231 (0.056) 0.002 0.034 0.003
194 210 (0.069) 0.003 0.016 0.049
195 240 (0.046) 0.002 0.010 0.004
196 207 (0.047) 0.002 0.003 0.060
197 198 (0.045) 0.917 0.002 0.002
198 185 (0.042) 0.045 0.002 0.002
199
200 Locus 3 : L3
201 3 alleles
202 0.0% missing data
203 266 (0.819) 0.034 0.950 0.993
204 272 (0.103) 0.004 0.045 0.004
205 278 (0.078) 0.962 0.004 0.003
206
207 Locus 4 : L4
208 19 alleles
209 0.0% missing data
210 164 (0.088) 0.004 0.107 0.161
211 173 (0.076) 0.003 0.519 0.003
212 182 (0.056) 0.002 0.108 0.002
213 170 (0.056) 0.002 0.011 0.041
214 200 (0.047) 0.002 0.027 0.002
215 202 (0.041) 0.002 0.010 0.002
216 176 (0.041) 0.002 0.010 0.002
217 185 (0.049) 0.002 0.035 0.002
218 167 (0.069) 0.003 0.035 0.061
219 158 (0.079) 0.003 0.078 0.075
220 155 (0.063) 0.003 0.023 0.052
221 152 (0.052) 0.002 0.007 0.184
222 179 (0.042) 0.002 0.010 0.003
223 145 (0.041) 0.002 0.010 0.002
224 149 (0.044) 0.002 0.002 0.193
225 161 (0.045) 0.002 0.002 0.211
226 136 (0.038) 0.874 0.002 0.002
227 101 (0.037) 0.045 0.002 0.002
228 139 (0.038) 0.045 0.002 0.002
229
230 Locus 5 : L5
231 24 alleles
232 0.0% missing data
233 182 (0.051) 0.089 0.083 0.002
234 188 (0.038) 0.002 0.050 0.002
235 185 (0.040) 0.002 0.114 0.002
236 194 (0.037) 0.002 0.042 0.001
237 209 (0.031) 0.001 0.010 0.001
238 191 (0.037) 0.002 0.042 0.001
239 160 (0.064) 0.267 0.035 0.060
240 200 (0.035) 0.001 0.034 0.001
241 173 (0.051) 0.089 0.091 0.002
242 176 (0.036) 0.001 0.034 0.002
243 169 (0.035) 0.001 0.034 0.002
244 131 (0.031) 0.001 0.010 0.001
245 166 (0.037) 0.001 0.050 0.002
246 154 (0.052) 0.002 0.050 0.063
247 144 (0.054) 0.002 0.053 0.207
248 157 (0.050) 0.002 0.026 0.100
249 203 (0.034) 0.001 0.018 0.001
250 147 (0.051) 0.002 0.047 0.069
251 134 (0.057) 0.002 0.096 0.280
252 141 (0.052) 0.002 0.043 0.118
253 206 (0.035) 0.001 0.034 0.002
254 151 (0.032) 0.001 0.002 0.059
255 137 (0.030) 0.001 0.002 0.020
256 179 (0.029) 0.521 0.002 0.001
257
258 Locus 6 : L6
259 6 alleles
260 11.6% missing data
261 177 (0.259) 0.264 0.195 0.111
262 165 (0.218) 0.224 0.200 0.030
263 171 (0.264) 0.275 0.591 0.012
264 175 (0.092) 0.085 0.005 0.542
265 183 (0.084) 0.077 0.004 0.163
266 179 (0.082) 0.075 0.004 0.143
267
268 Locus 7 : L7
269 10 alleles
270 0.0% missing data
271 187 (0.129) 0.005 0.408 0.005
272 191 (0.103) 0.004 0.198 0.004
273 183 (0.178) 0.007 0.157 0.498
274 195 (0.095) 0.004 0.142 0.004
275 199 (0.099) 0.004 0.037 0.023
276 180 (0.095) 0.004 0.021 0.062
277 203 (0.096) 0.004 0.020 0.103
278 206 (0.084) 0.003 0.011 0.161
279 214 (0.063) 0.003 0.003 0.137
280 138 (0.057) 0.961 0.003 0.002
281
282 Locus 8 : L8
283 7 alleles
284 0.0% missing data
285 151 (0.366) 0.015 0.624 0.666
286 148 (0.120) 0.005 0.063 0.024
287 145 (0.084) 0.963 0.010 0.003
288 157 (0.061) 0.002 0.011 0.003
289 155 (0.102) 0.004 0.119 0.004
290 135 (0.078) 0.003 0.036 0.003
291 141 (0.188) 0.008 0.137 0.297
292
293 Locus 9 : L9
294 10 alleles
295 0.0% missing data
296 138 (0.147) 0.006 0.549 0.006
297 140 (0.077) 0.003 0.052 0.003
298 147 (0.151) 0.966 0.133 0.007
299 142 (0.144) 0.006 0.079 0.341
300 145 (0.140) 0.006 0.089 0.117
301 136 (0.075) 0.003 0.044 0.003
302 134 (0.064) 0.003 0.019 0.003
303 132 (0.070) 0.003 0.027 0.004
304 153 (0.069) 0.003 0.004 0.415
305 149 (0.063) 0.003 0.003 0.101
306
307 Locus 10 : L10
308 7 alleles
309 0.0% missing data
310 313 (0.127) 0.005 0.112 0.005
311 317 (0.263) 0.011 0.700 0.011
312 321 (0.103) 0.004 0.054 0.004
313 319 (0.163) 0.447 0.063 0.008
314 325 (0.071) 0.003 0.012 0.003
315 306 (0.199) 0.008 0.055 0.967
316 324 (0.073) 0.522 0.004 0.003
317
318 Locus 11 : L11
319 8 alleles
320 0.0% missing data
321 250 (0.166) 0.007 0.439 0.007
322 247 (0.101) 0.004 0.085 0.004
323 242 (0.111) 0.004 0.125 0.005
324 251 (0.092) 0.004 0.060 0.005
325 245 (0.174) 0.007 0.120 0.106
326 257 (0.071) 0.003 0.020 0.003
327 243 (0.170) 0.966 0.018 0.864
328 253 (0.115) 0.005 0.133 0.006
329
330 Locus 12 : L12
331 4 alleles
332 0.0% missing data
333 204 (0.789) 0.949 0.973 0.836
334 180 (0.074) 0.003 0.020 0.003
335 218 (0.075) 0.003 0.004 0.158
336 210 (0.062) 0.045 0.003 0.003
337
338 Locus 13 : L13
339 6 alleles
340 0.0% missing data
341 260 (0.621) 0.855 0.892 0.888
342 263 (0.129) 0.092 0.079 0.005
343 257 (0.067) 0.003 0.020 0.003
344 269 (0.065) 0.003 0.003 0.080
345 275 (0.060) 0.002 0.003 0.022
346 246 (0.057) 0.045 0.003 0.002
347
348 Locus 14 : L14
349 5 alleles
350 0.0% missing data
351 157 (0.608) 0.984 0.660 0.886
352 146 (0.144) 0.006 0.288 0.006
353 153 (0.077) 0.003 0.028 0.003
354 155 (0.109) 0.004 0.021 0.083
355 163 (0.063) 0.003 0.003 0.022
356
357 Locus 15 : L15
358 2 alleles
359 0.0% missing data
360 243 (0.627) 0.945 0.883 0.027
361 238 (0.373) 0.055 0.117 0.973
362
363 Locus 16 : L16
364 3 alleles
365 0.0% missing data
366 173 (0.730) 0.989 0.838 0.863
367 165 (0.092) 0.004 0.053 0.004
368 169 (0.179) 0.007 0.109 0.133
369
370 Locus 17 : L17
371 2 alleles
372 0.0% missing data
373 171 (0.919) 0.038 0.996 0.997
374 168 (0.081) 0.962 0.004 0.003
375
376 Locus 18 : L18
377 4 alleles
378 0.0% missing data
379 286 (0.672) 0.027 0.874 0.964
380 287 (0.120) 0.005 0.095 0.005
381 283 (0.110) 0.005 0.020 0.028
382 290 (0.099) 0.963 0.011 0.004
383
384 Values of parameters used in structure:
385 DATAFILE= 34\project_data, OUTFILE= \Results\DAE Admix_run_54, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=3, 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
386 [STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9,