Mercurial > repos > iuc > structureharvester
comparison test-data/example_harvester_archive/K1ReRun_run_2_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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3 ---------------------------------------------------- | |
4 STRUCTURE by Pritchard, Stephens and Donnelly (2000) | |
5 and Falush, Stephens and Pritchard (2003) | |
6 Code by Pritchard and Falush | |
7 Version 2.2 (March 2007) | |
8 ---------------------------------------------------- | |
9 | |
10 | |
11 | |
12 Command line arguments: bin/structure.exe -m "/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/K1ReRun/mainparams" -e "/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/K1ReRun/extraparams" | |
13 Input File: \project_data | |
14 | |
15 Run parameters: | |
16 95 individuals | |
17 18 loci | |
18 1 populations assumed | |
19 50000 Burn-in period | |
20 500000 Reps | |
21 | |
22 | |
23 -------------------------------------------- | |
24 Proportion of membership of each pre-defined | |
25 population in each of the 1 clusters | |
26 | |
27 Given Inferred Clusters Number of | |
28 Pop 1 Individuals | |
29 | |
30 1: 1.000 6 | |
31 2: 1.000 6 | |
32 3: 1.000 6 | |
33 4: 1.000 6 | |
34 5: 1.000 6 | |
35 6: 1.000 6 | |
36 7: 1.000 6 | |
37 8: 1.000 6 | |
38 9: 1.000 6 | |
39 10: 1.000 6 | |
40 11: 1.000 6 | |
41 12: 1.000 6 | |
42 13: 1.000 6 | |
43 14: 1.000 6 | |
44 15: 1.000 6 | |
45 16: 1.000 5 | |
46 -------------------------------------------- | |
47 | |
48 Allele-freq. divergence among pops (Net nucleotide distance), | |
49 computed using point estimates of P. | |
50 | |
51 1 | |
52 1 - | |
53 | |
54 Average distances (expected heterozygosity) between individuals in same cluster: | |
55 cluster 1 : -122.5537 | |
56 | |
57 -------------------------------------------- | |
58 Estimated Ln Prob of Data = -4330.0 | |
59 Mean value of ln likelihood = -4300.2 | |
60 Variance of ln likelihood = 59.7 | |
61 | |
62 Mean value of Fst_1 = 0.0009 | |
63 | |
64 | |
65 Inferred ancestry of individuals: | |
66 Label (%Miss) Pop: Inferred clusters | |
67 1 99-70-01 (0) 1 : 1.000 | |
68 2 99-70-02 (0) 1 : 1.000 | |
69 3 99-70-03 (0) 1 : 1.000 | |
70 4 99-70-04 (0) 1 : 1.000 | |
71 5 99-70-05 (0) 1 : 1.000 | |
72 6 99-70-24 (0) 1 : 1.000 | |
73 7 En_466 (0) 2 : 1.000 | |
74 8 En_479 (0) 2 : 1.000 | |
75 9 En_480 (0) 2 : 1.000 | |
76 10 En_482 (0) 2 : 1.000 | |
77 11 En_484 (0) 2 : 1.000 | |
78 12 En_485 (0) 2 : 1.000 | |
79 13 99-69-02 (0) 3 : 1.000 | |
80 14 99-69-05 (0) 3 : 1.000 | |
81 15 99-69-14 (0) 3 : 1.000 | |
82 16 99-69-30 (0) 3 : 1.000 | |
83 17 99-69-31 (0) 3 : 1.000 | |
84 18 99-69-40 (0) 3 : 1.000 | |
85 19 99-72-08 (0) 4 : 1.000 | |
86 20 99-72-09 (0) 4 : 1.000 | |
87 21 99-72-13 (0) 4 : 1.000 | |
88 22 99-72-21 (0) 4 : 1.000 | |
89 23 99-72-25 (0) 4 : 1.000 | |
90 24 99-72-30 (0) 4 : 1.000 | |
91 25 99-78-01 (0) 5 : 1.000 | |
92 26 99-78-02 (0) 5 : 1.000 | |
93 27 99-78-03 (0) 5 : 1.000 | |
94 28 99-78-04 (0) 5 : 1.000 | |
95 29 99-78-05 (0) 5 : 1.000 | |
96 30 99-78-06 (0) 5 : 1.000 | |
97 31 99-83-03 (0) 6 : 1.000 | |
98 32 99-83-05 (0) 6 : 1.000 | |
99 33 99-83-08 (0) 6 : 1.000 | |
100 34 99-83-14 (0) 6 : 1.000 | |
101 35 99-83-25 (0) 6 : 1.000 | |
102 36 99-83-35 (0) 6 : 1.000 | |
103 37 En_360 (0) 7 : 1.000 | |
104 38 En_365 (0) 7 : 1.000 | |
105 39 En_367 (0) 7 : 1.000 | |
106 40 En_370 (0) 7 : 1.000 | |
107 41 En_371 (0) 7 : 1.000 | |
108 42 En_372 (0) 7 : 1.000 | |
109 43 En_341 (0) 8 : 1.000 | |
110 44 En_342 (0) 8 : 1.000 | |
111 45 En_343 (0) 8 : 1.000 | |
112 46 En_345 (0) 8 : 1.000 | |
113 47 En_346 (0) 8 : 1.000 | |
114 48 En_349 (0) 8 : 1.000 | |
115 49 En_121 (0) 9 : 1.000 | |
116 50 En_122 (0) 9 : 1.000 | |
117 51 En_125 (0) 9 : 1.000 | |
118 52 En_127 (0) 9 : 1.000 | |
119 53 En_128 (0) 9 : 1.000 | |
120 54 En_129 (0) 9 : 1.000 | |
121 55 En_306 (0) 10 : 1.000 | |
122 56 En_310 (0) 10 : 1.000 | |
123 57 En_312 (0) 10 : 1.000 | |
124 58 En_313 (0) 10 : 1.000 | |
125 59 En_317 (0) 10 : 1.000 | |
126 60 En_318 (0) 10 : 1.000 | |
127 61 99-45-19 (0) 11 : 1.000 | |
128 62 99-45-20 (0) 11 : 1.000 | |
129 63 99-45-21 (0) 11 : 1.000 | |
130 64 99-45-22 (0) 11 : 1.000 | |
131 65 99-45-23 (0) 11 : 1.000 | |
132 66 99-45-24 (0) 11 : 1.000 | |
133 67 98-123-01 (0) 12 : 1.000 | |
134 68 98-123-02 (0) 12 : 1.000 | |
135 69 98-123-03 (0) 12 : 1.000 | |
136 70 98-123-04 (0) 12 : 1.000 | |
137 71 98-123-05 (0) 12 : 1.000 | |
138 72 98-123-12 (0) 12 : 1.000 | |
139 73 99-93-20 (0) 13 : 1.000 | |
140 74 99-93-21 (0) 13 : 1.000 | |
141 75 99-93-23 (0) 13 : 1.000 | |
142 76 99-93-24 (0) 13 : 1.000 | |
143 77 99-93-25 (0) 13 : 1.000 | |
144 78 99-93-26 (0) 13 : 1.000 | |
145 79 99-21-02 (0) 14 : 1.000 | |
146 80 99-21-04 (0) 14 : 1.000 | |
147 81 99-21-05 (0) 14 : 1.000 | |
148 82 99-21-08 (0) 14 : 1.000 | |
149 83 99-21-09 (0) 14 : 1.000 | |
150 84 99-21-10 (0) 14 : 1.000 | |
151 85 01-58-20 (5) 15 : 1.000 | |
152 86 01-58-33 (5) 15 : 1.000 | |
153 87 01-58-34 (5) 15 : 1.000 | |
154 88 01-58-35 (5) 15 : 1.000 | |
155 89 01-58-53 (5) 15 : 1.000 | |
156 90 01-58-56 (5) 15 : 1.000 | |
157 91 98-116-04 (5) 16 : 1.000 | |
158 92 98-116-07 (5) 16 : 1.000 | |
159 93 98-116-14 (5) 16 : 1.000 | |
160 94 98-116-26 (5) 16 : 1.000 | |
161 95 98-116-27 (5) 16 : 1.000 | |
162 | |
163 | |
164 Estimated Allele Frequencies in each cluster | |
165 First column gives estimated ancestral frequencies | |
166 | |
167 | |
168 Locus 1 : TAGA40 | |
169 7 alleles | |
170 0.0% missing data | |
171 118 (0.591) 0.594 | |
172 127 (0.072) 0.071 | |
173 130 (0.077) 0.077 | |
174 114 (0.031) 0.030 | |
175 122 (0.092) 0.091 | |
176 110 (0.076) 0.076 | |
177 135 (0.061) 0.061 | |
178 | |
179 Locus 2 : B113 | |
180 15 alleles | |
181 0.0% missing data | |
182 228 (0.097) 0.097 | |
183 222 (0.117) 0.117 | |
184 225 (0.155) 0.156 | |
185 234 (0.015) 0.015 | |
186 219 (0.141) 0.142 | |
187 213 (0.217) 0.219 | |
188 204 (0.011) 0.010 | |
189 216 (0.035) 0.034 | |
190 195 (0.015) 0.015 | |
191 231 (0.025) 0.024 | |
192 210 (0.025) 0.024 | |
193 240 (0.010) 0.010 | |
194 207 (0.020) 0.019 | |
195 198 (0.107) 0.107 | |
196 185 (0.010) 0.010 | |
197 | |
198 Locus 3 : B117 | |
199 3 alleles | |
200 0.0% missing data | |
201 266 (0.848) 0.849 | |
202 272 (0.032) 0.031 | |
203 278 (0.120) 0.120 | |
204 | |
205 Locus 4 : ATG16.1 | |
206 19 alleles | |
207 0.0% missing data | |
208 164 (0.104) 0.105 | |
209 173 (0.307) 0.311 | |
210 182 (0.067) 0.067 | |
211 170 (0.020) 0.019 | |
212 200 (0.020) 0.019 | |
213 202 (0.010) 0.010 | |
214 176 (0.010) 0.010 | |
215 185 (0.024) 0.024 | |
216 167 (0.039) 0.038 | |
217 158 (0.067) 0.067 | |
218 155 (0.029) 0.029 | |
219 152 (0.053) 0.053 | |
220 179 (0.010) 0.010 | |
221 145 (0.010) 0.010 | |
222 149 (0.053) 0.053 | |
223 161 (0.057) 0.057 | |
224 136 (0.100) 0.100 | |
225 101 (0.010) 0.010 | |
226 139 (0.010) 0.009 | |
227 | |
228 Locus 5 : ATG17 | |
229 24 alleles | |
230 0.0% missing data | |
231 182 (0.060) 0.061 | |
232 188 (0.033) 0.033 | |
233 185 (0.070) 0.070 | |
234 194 (0.028) 0.028 | |
235 209 (0.010) 0.009 | |
236 191 (0.028) 0.028 | |
237 160 (0.065) 0.065 | |
238 200 (0.024) 0.023 | |
239 173 (0.065) 0.065 | |
240 176 (0.024) 0.023 | |
241 169 (0.024) 0.023 | |
242 131 (0.010) 0.009 | |
243 166 (0.033) 0.033 | |
244 154 (0.047) 0.047 | |
245 144 (0.083) 0.084 | |
246 157 (0.042) 0.042 | |
247 203 (0.015) 0.014 | |
248 147 (0.047) 0.047 | |
249 134 (0.125) 0.126 | |
250 141 (0.056) 0.056 | |
251 206 (0.024) 0.024 | |
252 151 (0.019) 0.019 | |
253 137 (0.010) 0.009 | |
254 179 (0.060) 0.061 | |
255 | |
256 Locus 6 : ENE2 | |
257 6 alleles | |
258 11.6% missing data | |
259 177 (0.166) 0.166 | |
260 165 (0.150) 0.150 | |
261 171 (0.424) 0.425 | |
262 175 (0.161) 0.161 | |
263 183 (0.052) 0.052 | |
264 179 (0.047) 0.046 | |
265 | |
266 Locus 7 : CATG2 | |
267 10 alleles | |
268 0.0% missing data | |
269 187 (0.253) 0.255 | |
270 191 (0.125) 0.125 | |
271 183 (0.223) 0.225 | |
272 195 (0.090) 0.090 | |
273 199 (0.030) 0.030 | |
274 180 (0.031) 0.030 | |
275 203 (0.041) 0.040 | |
276 206 (0.050) 0.050 | |
277 214 (0.041) 0.040 | |
278 138 (0.115) 0.115 | |
279 | |
280 Locus 8 : ATG13 | |
281 7 alleles | |
282 0.0% missing data | |
283 151 (0.556) 0.558 | |
284 148 (0.046) 0.046 | |
285 145 (0.122) 0.122 | |
286 157 (0.011) 0.010 | |
287 155 (0.077) 0.076 | |
288 135 (0.026) 0.026 | |
289 141 (0.162) 0.162 | |
290 | |
291 Locus 9 : TAGA11 | |
292 10 alleles | |
293 0.0% missing data | |
294 138 (0.343) 0.346 | |
295 140 (0.035) 0.035 | |
296 147 (0.194) 0.195 | |
297 142 (0.135) 0.135 | |
298 145 (0.085) 0.085 | |
299 136 (0.030) 0.030 | |
300 134 (0.016) 0.015 | |
301 132 (0.021) 0.020 | |
302 153 (0.110) 0.110 | |
303 149 (0.031) 0.030 | |
304 | |
305 Locus 10 : A018 | |
306 7 alleles | |
307 0.0% missing data | |
308 313 (0.071) 0.071 | |
309 317 (0.435) 0.437 | |
310 321 (0.036) 0.036 | |
311 319 (0.092) 0.091 | |
312 325 (0.011) 0.010 | |
313 306 (0.289) 0.290 | |
314 324 (0.066) 0.066 | |
315 | |
316 Locus 11 : A019 | |
317 8 alleles | |
318 0.0% missing data | |
319 250 (0.276) 0.277 | |
320 247 (0.056) 0.056 | |
321 242 (0.081) 0.081 | |
322 251 (0.041) 0.040 | |
323 245 (0.102) 0.101 | |
324 257 (0.016) 0.015 | |
325 243 (0.342) 0.343 | |
326 253 (0.086) 0.086 | |
327 | |
328 Locus 12 : ATG26 | |
329 4 alleles | |
330 0.0% missing data | |
331 204 (0.926) 0.928 | |
332 180 (0.016) 0.015 | |
333 218 (0.047) 0.046 | |
334 210 (0.011) 0.010 | |
335 | |
336 Locus 13 : C111 | |
337 6 alleles | |
338 0.0% missing data | |
339 260 (0.873) 0.877 | |
340 263 (0.062) 0.061 | |
341 257 (0.016) 0.015 | |
342 269 (0.026) 0.026 | |
343 275 (0.011) 0.010 | |
344 246 (0.011) 0.010 | |
345 | |
346 Locus 14 : ENE3 | |
347 5 alleles | |
348 0.0% missing data | |
349 157 (0.747) 0.749 | |
350 146 (0.185) 0.185 | |
351 153 (0.021) 0.020 | |
352 155 (0.037) 0.036 | |
353 163 (0.011) 0.010 | |
354 | |
355 Locus 15 : ENE4 | |
356 2 alleles | |
357 0.0% missing data | |
358 243 (0.672) 0.672 | |
359 238 (0.328) 0.328 | |
360 | |
361 Locus 16 : CATG14 | |
362 3 alleles | |
363 0.0% missing data | |
364 173 (0.859) 0.860 | |
365 165 (0.037) 0.036 | |
366 169 (0.104) 0.104 | |
367 | |
368 Locus 17 : ATG18 | |
369 2 alleles | |
370 0.0% missing data | |
371 171 (0.880) 0.880 | |
372 168 (0.120) 0.120 | |
373 | |
374 Locus 18 : C114 | |
375 4 alleles | |
376 0.0% missing data | |
377 286 (0.792) 0.794 | |
378 287 (0.062) 0.061 | |
379 283 (0.022) 0.021 | |
380 290 (0.124) 0.124 | |
381 | |
382 Values of parameters used in structure: | |
383 DATAFILE=/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/project_data, OUTFILE=/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/K1ReRun/Results/K1ReRun_run_2, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=1, 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, PRINTNET=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, SEED=1213374129, 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, |