Mercurial > repos > iuc > structureharvester
comparison test-data/example_harvester_archive/Admix_run_001_f @ 0:8a7390c4d6bf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
author | iuc |
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date | Mon, 11 Dec 2017 04:37:17 -0500 |
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-1:000000000000 | 0:8a7390c4d6bf |
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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, |