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comparison test-data/example_harvester_archive/Admix_run_004_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: 0.002 0.997 0.001 6
32 2: 0.002 0.997 0.002 6
33 3: 0.002 0.997 0.001 6
34 4: 0.003 0.996 0.001 6
35 5: 0.003 0.995 0.002 6
36 6: 0.016 0.981 0.003 6
37 7: 0.002 0.996 0.001 6
38 8: 0.004 0.994 0.002 6
39 9: 0.038 0.961 0.002 6
40 10: 0.082 0.913 0.005 6
41 11: 0.995 0.004 0.001 6
42 12: 0.997 0.002 0.001 6
43 13: 0.997 0.002 0.001 6
44 14: 0.997 0.002 0.001 6
45 15: 0.001 0.001 0.998 6
46 16: 0.002 0.001 0.997 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 - 1.29 2.61
54 2 1.55 - 2.34
55 3 3.44 2.90 -
56 --------------------------------------------
57 Estimated Ln Prob of Data = -3020.8
58 Mean value of ln likelihood = -2945.8
59 Variance of ln likelihood = 150.0
60 Mean value of alpha = 0.0269
61
62 Mean value of Fst_1 = 0.3266
63 Mean value of Fst_2 = 0.1332
64 Mean value of Fst_3 = 0.5223
65
66
67 Inferred ancestry of individuals:
68 Label (%Miss) Pop: Inferred clusters
69 1 A01 (0) 1 : 0.002 0.997 0.001
70 2 A02 (0) 1 : 0.002 0.997 0.001
71 3 A03 (0) 1 : 0.002 0.997 0.001
72 4 A04 (0) 1 : 0.002 0.997 0.001
73 5 A05 (0) 1 : 0.002 0.996 0.001
74 6 A24 (0) 1 : 0.002 0.997 0.001
75 7 B466 (0) 2 : 0.002 0.997 0.001
76 8 B479 (0) 2 : 0.002 0.997 0.001
77 9 B480 (0) 2 : 0.002 0.997 0.001
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 : 0.002 0.997 0.001
81 13 C02 (0) 3 : 0.002 0.997 0.001
82 14 C05 (0) 3 : 0.002 0.997 0.001
83 15 C14 (0) 3 : 0.001 0.997 0.001
84 16 C30 (0) 3 : 0.002 0.997 0.001
85 17 C31 (0) 3 : 0.002 0.997 0.001
86 18 C40 (0) 3 : 0.002 0.997 0.001
87 19 D08 (0) 4 : 0.001 0.997 0.001
88 20 D09 (0) 4 : 0.003 0.996 0.001
89 21 D13 (0) 4 : 0.002 0.996 0.002
90 22 D21 (0) 4 : 0.006 0.993 0.002
91 23 D25 (0) 4 : 0.003 0.996 0.001
92 24 D30 (0) 4 : 0.003 0.995 0.001
93 25 E01 (0) 5 : 0.004 0.994 0.002
94 26 E02 (0) 5 : 0.004 0.994 0.002
95 27 E03 (0) 5 : 0.003 0.996 0.001
96 28 E04 (0) 5 : 0.002 0.996 0.001
97 29 E05 (0) 5 : 0.002 0.996 0.001
98 30 E06 (0) 5 : 0.004 0.994 0.001
99 31 F03 (0) 6 : 0.003 0.985 0.012
100 32 F05 (0) 6 : 0.033 0.966 0.001
101 33 F08 (0) 6 : 0.015 0.982 0.002
102 34 F14 (0) 6 : 0.038 0.961 0.001
103 35 F25 (0) 6 : 0.005 0.994 0.001
104 36 F35 (0) 6 : 0.004 0.995 0.001
105 37 B360 (0) 7 : 0.002 0.997 0.001
106 38 B365 (0) 7 : 0.004 0.995 0.001
107 39 B367 (0) 7 : 0.002 0.997 0.001
108 40 B370 (0) 7 : 0.003 0.996 0.001
109 41 B371 (0) 7 : 0.003 0.996 0.001
110 42 B372 (0) 7 : 0.002 0.997 0.001
111 43 B341 (0) 8 : 0.008 0.985 0.007
112 44 B342 (0) 8 : 0.004 0.995 0.001
113 45 B343 (0) 8 : 0.002 0.996 0.001
114 46 B345 (0) 8 : 0.004 0.995 0.001
115 47 B346 (0) 8 : 0.002 0.997 0.001
116 48 B349 (0) 8 : 0.002 0.996 0.001
117 49 B121 (0) 9 : 0.007 0.991 0.002
118 50 B122 (0) 9 : 0.122 0.877 0.001
119 51 B125 (0) 9 : 0.005 0.993 0.002
120 52 B127 (0) 9 : 0.007 0.992 0.001
121 53 B128 (0) 9 : 0.026 0.973 0.002
122 54 B129 (0) 9 : 0.060 0.938 0.002
123 55 B306 (0) 10 : 0.011 0.974 0.015
124 56 B310 (0) 10 : 0.101 0.898 0.001
125 57 B312 (0) 10 : 0.176 0.822 0.002
126 58 B313 (0) 10 : 0.132 0.859 0.009
127 59 B317 (0) 10 : 0.053 0.945 0.001
128 60 B318 (0) 10 : 0.018 0.978 0.004
129 61 G19 (0) 11 : 0.997 0.002 0.001
130 62 G20 (0) 11 : 0.997 0.002 0.001
131 63 G21 (0) 11 : 0.997 0.002 0.001
132 64 G22 (0) 11 : 0.986 0.013 0.001
133 65 G23 (0) 11 : 0.996 0.003 0.001
134 66 G24 (0) 11 : 0.997 0.002 0.001
135 67 H01 (0) 12 : 0.997 0.002 0.001
136 68 H02 (0) 12 : 0.997 0.002 0.001
137 69 H03 (0) 12 : 0.997 0.002 0.001
138 70 H04 (0) 12 : 0.997 0.002 0.001
139 71 H05 (0) 12 : 0.997 0.002 0.001
140 72 H12 (0) 12 : 0.997 0.001 0.001
141 73 I20 (0) 13 : 0.997 0.002 0.001
142 74 I21 (0) 13 : 0.997 0.002 0.001
143 75 I23 (0) 13 : 0.993 0.004 0.002
144 76 I24 (0) 13 : 0.997 0.002 0.001
145 77 I25 (0) 13 : 0.997 0.002 0.001
146 78 I26 (0) 13 : 0.997 0.002 0.001
147 79 J02 (0) 14 : 0.997 0.002 0.001
148 80 J04 (0) 14 : 0.997 0.002 0.001
149 81 J05 (0) 14 : 0.997 0.002 0.001
150 82 J08 (0) 14 : 0.995 0.004 0.001
151 83 J09 (0) 14 : 0.997 0.002 0.001
152 84 J10 (0) 14 : 0.997 0.001 0.001
153 85 K20 (5) 15 : 0.001 0.001 0.998
154 86 K33 (5) 15 : 0.001 0.001 0.998
155 87 K34 (5) 15 : 0.001 0.001 0.998
156 88 K35 (5) 15 : 0.001 0.001 0.998
157 89 K53 (5) 15 : 0.001 0.001 0.998
158 90 K56 (5) 15 : 0.001 0.001 0.998
159 91 L04 (5) 16 : 0.001 0.001 0.998
160 92 L07 (5) 16 : 0.001 0.001 0.998
161 93 L14 (5) 16 : 0.005 0.002 0.993
162 94 L26 (5) 16 : 0.001 0.001 0.998
163 95 L27 (5) 16 : 0.001 0.001 0.998
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 (0.408) 0.476 0.761 0.017
174 127 (0.105) 0.004 0.110 0.004
175 130 (0.114) 0.005 0.029 0.486
176 114 (0.084) 0.003 0.045 0.003
177 122 (0.142) 0.243 0.045 0.006
178 110 (0.084) 0.266 0.007 0.003
179 135 (0.064) 0.003 0.003 0.481
180
181 Locus 2 : L2
182 15 alleles
183 0.0% missing data
184 228 (0.070) 0.003 0.156 0.003
185 222 (0.102) 0.041 0.174 0.004
186 225 (0.077) 0.003 0.252 0.003
187 234 (0.050) 0.002 0.019 0.002
188 219 (0.111) 0.142 0.173 0.005
189 213 (0.113) 0.604 0.109 0.005
190 204 (0.046) 0.002 0.010 0.002
191 216 (0.075) 0.081 0.020 0.003
192 195 (0.051) 0.002 0.019 0.002
193 231 (0.055) 0.003 0.035 0.002
194 210 (0.071) 0.049 0.016 0.003
195 240 (0.046) 0.004 0.010 0.002
196 207 (0.048) 0.060 0.003 0.002
197 198 (0.045) 0.002 0.002 0.917
198 185 (0.042) 0.002 0.002 0.045
199
200 Locus 3 : L3
201 3 alleles
202 0.0% missing data
203 266 (0.818) 0.993 0.950 0.033
204 272 (0.103) 0.004 0.045 0.004
205 278 (0.078) 0.003 0.004 0.962
206
207 Locus 4 : L4
208 19 alleles
209 0.0% missing data
210 164 (0.086) 0.160 0.107 0.004
211 173 (0.074) 0.003 0.519 0.003
212 182 (0.056) 0.002 0.108 0.002
213 170 (0.058) 0.041 0.011 0.002
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 (0.047) 0.002 0.035 0.002
218 167 (0.069) 0.061 0.035 0.003
219 158 (0.080) 0.075 0.078 0.003
220 155 (0.066) 0.052 0.023 0.003
221 152 (0.053) 0.184 0.007 0.002
222 179 (0.041) 0.003 0.010 0.002
223 145 (0.040) 0.002 0.010 0.002
224 149 (0.044) 0.192 0.002 0.002
225 161 (0.044) 0.212 0.002 0.002
226 136 (0.039) 0.002 0.002 0.874
227 101 (0.038) 0.002 0.002 0.045
228 139 (0.037) 0.002 0.002 0.045
229
230 Locus 5 : L5
231 24 alleles
232 0.0% missing data
233 182 (0.050) 0.002 0.083 0.089
234 188 (0.038) 0.002 0.050 0.002
235 185 (0.041) 0.002 0.115 0.002
236 194 (0.037) 0.001 0.042 0.001
237 209 (0.031) 0.001 0.010 0.001
238 191 (0.036) 0.001 0.042 0.001
239 160 (0.062) 0.060 0.035 0.267
240 200 (0.036) 0.001 0.034 0.001
241 173 (0.050) 0.002 0.091 0.089
242 176 (0.036) 0.002 0.034 0.001
243 169 (0.037) 0.002 0.034 0.001
244 131 (0.032) 0.001 0.010 0.001
245 166 (0.038) 0.002 0.050 0.002
246 154 (0.052) 0.063 0.050 0.002
247 144 (0.053) 0.208 0.053 0.002
248 157 (0.049) 0.100 0.026 0.002
249 203 (0.033) 0.001 0.018 0.001
250 147 (0.052) 0.069 0.047 0.002
251 134 (0.058) 0.279 0.096 0.002
252 141 (0.052) 0.118 0.043 0.002
253 206 (0.036) 0.002 0.034 0.001
254 151 (0.032) 0.059 0.002 0.001
255 137 (0.030) 0.020 0.002 0.001
256 179 (0.029) 0.001 0.002 0.522
257
258 Locus 6 : L6
259 6 alleles
260 11.6% missing data
261 177 (0.259) 0.111 0.195 0.264
262 165 (0.219) 0.030 0.201 0.225
263 171 (0.262) 0.012 0.591 0.273
264 175 (0.092) 0.542 0.005 0.085
265 183 (0.084) 0.163 0.004 0.076
266 179 (0.084) 0.143 0.004 0.077
267
268 Locus 7 : L7
269 10 alleles
270 0.0% missing data
271 187 (0.127) 0.005 0.408 0.005
272 191 (0.105) 0.004 0.198 0.004
273 183 (0.178) 0.498 0.157 0.007
274 195 (0.095) 0.004 0.142 0.004
275 199 (0.100) 0.023 0.038 0.004
276 180 (0.096) 0.062 0.021 0.004
277 203 (0.095) 0.103 0.020 0.004
278 206 (0.084) 0.161 0.011 0.003
279 214 (0.064) 0.137 0.003 0.003
280 138 (0.058) 0.002 0.003 0.961
281
282 Locus 8 : L8
283 7 alleles
284 0.0% missing data
285 151 (0.366) 0.666 0.624 0.015
286 148 (0.120) 0.024 0.063 0.005
287 145 (0.085) 0.003 0.011 0.963
288 157 (0.062) 0.003 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 (0.187) 0.297 0.137 0.008
292
293 Locus 9 : L9
294 10 alleles
295 0.0% missing data
296 138 (0.146) 0.006 0.549 0.006
297 140 (0.078) 0.003 0.052 0.003
298 147 (0.151) 0.007 0.134 0.966
299 142 (0.146) 0.341 0.079 0.006
300 145 (0.138) 0.117 0.089 0.006
301 136 (0.075) 0.003 0.044 0.003
302 134 (0.065) 0.003 0.019 0.003
303 132 (0.070) 0.004 0.027 0.003
304 153 (0.069) 0.415 0.004 0.003
305 149 (0.063) 0.101 0.003 0.003
306
307 Locus 10 : L10
308 7 alleles
309 0.0% missing data
310 313 (0.126) 0.005 0.112 0.005
311 317 (0.261) 0.011 0.700 0.011
312 321 (0.103) 0.004 0.054 0.004
313 319 (0.163) 0.008 0.063 0.447
314 325 (0.071) 0.003 0.012 0.003
315 306 (0.202) 0.966 0.055 0.008
316 324 (0.073) 0.003 0.004 0.522
317
318 Locus 11 : L11
319 8 alleles
320 0.0% missing data
321 250 (0.165) 0.007 0.438 0.007
322 247 (0.100) 0.004 0.085 0.004
323 242 (0.111) 0.005 0.125 0.004
324 251 (0.094) 0.005 0.060 0.004
325 245 (0.173) 0.106 0.120 0.007
326 257 (0.072) 0.003 0.020 0.003
327 243 (0.171) 0.864 0.018 0.966
328 253 (0.115) 0.006 0.133 0.005
329
330 Locus 12 : L12
331 4 alleles
332 0.0% missing data
333 204 (0.791) 0.836 0.973 0.949
334 180 (0.074) 0.003 0.020 0.003
335 218 (0.075) 0.158 0.004 0.003
336 210 (0.060) 0.003 0.003 0.045
337
338 Locus 13 : L13
339 6 alleles
340 0.0% missing data
341 260 (0.615) 0.888 0.891 0.854
342 263 (0.131) 0.005 0.079 0.092
343 257 (0.069) 0.003 0.020 0.003
344 269 (0.067) 0.080 0.004 0.003
345 275 (0.061) 0.022 0.003 0.002
346 246 (0.057) 0.002 0.003 0.045
347
348 Locus 14 : L14
349 5 alleles
350 0.0% missing data
351 157 (0.607) 0.886 0.660 0.984
352 146 (0.143) 0.006 0.287 0.006
353 153 (0.076) 0.003 0.028 0.003
354 155 (0.110) 0.083 0.021 0.004
355 163 (0.063) 0.022 0.003 0.003
356
357 Locus 15 : L15
358 2 alleles
359 0.0% missing data
360 243 (0.625) 0.027 0.884 0.945
361 238 (0.375) 0.973 0.116 0.055
362
363 Locus 16 : L16
364 3 alleles
365 0.0% missing data
366 173 (0.728) 0.863 0.838 0.989
367 165 (0.091) 0.004 0.053 0.004
368 169 (0.181) 0.133 0.109 0.007
369
370 Locus 17 : L17
371 2 alleles
372 0.0% missing data
373 171 (0.919) 0.997 0.996 0.038
374 168 (0.081) 0.003 0.004 0.962
375
376 Locus 18 : L18
377 4 alleles
378 0.0% missing data
379 286 (0.673) 0.963 0.874 0.027
380 287 (0.119) 0.005 0.095 0.005
381 283 (0.109) 0.028 0.020 0.005
382 290 (0.099) 0.004 0.011 0.963
383
384 Values of parameters used in structure:
385 DATAFILE= 34\project_data, OUTFILE= \Results\DAE Admix_run_6, 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,