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comparison test-data/example_harvester_archive/K1ReRun_run_2_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 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,