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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit f1cac0ad033da79288fe720fbe5af5948cc61d44
| author | iuc |
|---|---|
| date | Wed, 25 Sep 2024 15:36:50 +0000 |
| parents | 8a7390c4d6bf |
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---------------------------------------------------- STRUCTURE by Pritchard, Stephens and Donnelly (2000) and Falush, Stephens and Pritchard (2003) Code by Pritchard and Falush Version 2.2 (March 2007) ---------------------------------------------------- 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" Input File: \project_data Run parameters: 95 individuals 18 loci 1 populations assumed 50000 Burn-in period 500000 Reps -------------------------------------------- Proportion of membership of each pre-defined population in each of the 1 clusters Given Inferred Clusters Number of Pop 1 Individuals 1: 1.000 6 2: 1.000 6 3: 1.000 6 4: 1.000 6 5: 1.000 6 6: 1.000 6 7: 1.000 6 8: 1.000 6 9: 1.000 6 10: 1.000 6 11: 1.000 6 12: 1.000 6 13: 1.000 6 14: 1.000 6 15: 1.000 6 16: 1.000 5 -------------------------------------------- Allele-freq. divergence among pops (Net nucleotide distance), computed using point estimates of P. 1 1 - Average distances (expected heterozygosity) between individuals in same cluster: cluster 1 : -122.5714 -------------------------------------------- Estimated Ln Prob of Data = -4329.9 Mean value of ln likelihood = -4300.3 Variance of ln likelihood = 59.2 Mean value of Fst_1 = 0.0012 Inferred ancestry of individuals: Label (%Miss) Pop: Inferred clusters 1 99-70-01 (0) 1 : 1.000 2 99-70-02 (0) 1 : 1.000 3 99-70-03 (0) 1 : 1.000 4 99-70-04 (0) 1 : 1.000 5 99-70-05 (0) 1 : 1.000 6 99-70-24 (0) 1 : 1.000 7 En_466 (0) 2 : 1.000 8 En_479 (0) 2 : 1.000 9 En_480 (0) 2 : 1.000 10 En_482 (0) 2 : 1.000 11 En_484 (0) 2 : 1.000 12 En_485 (0) 2 : 1.000 13 99-69-02 (0) 3 : 1.000 14 99-69-05 (0) 3 : 1.000 15 99-69-14 (0) 3 : 1.000 16 99-69-30 (0) 3 : 1.000 17 99-69-31 (0) 3 : 1.000 18 99-69-40 (0) 3 : 1.000 19 99-72-08 (0) 4 : 1.000 20 99-72-09 (0) 4 : 1.000 21 99-72-13 (0) 4 : 1.000 22 99-72-21 (0) 4 : 1.000 23 99-72-25 (0) 4 : 1.000 24 99-72-30 (0) 4 : 1.000 25 99-78-01 (0) 5 : 1.000 26 99-78-02 (0) 5 : 1.000 27 99-78-03 (0) 5 : 1.000 28 99-78-04 (0) 5 : 1.000 29 99-78-05 (0) 5 : 1.000 30 99-78-06 (0) 5 : 1.000 31 99-83-03 (0) 6 : 1.000 32 99-83-05 (0) 6 : 1.000 33 99-83-08 (0) 6 : 1.000 34 99-83-14 (0) 6 : 1.000 35 99-83-25 (0) 6 : 1.000 36 99-83-35 (0) 6 : 1.000 37 En_360 (0) 7 : 1.000 38 En_365 (0) 7 : 1.000 39 En_367 (0) 7 : 1.000 40 En_370 (0) 7 : 1.000 41 En_371 (0) 7 : 1.000 42 En_372 (0) 7 : 1.000 43 En_341 (0) 8 : 1.000 44 En_342 (0) 8 : 1.000 45 En_343 (0) 8 : 1.000 46 En_345 (0) 8 : 1.000 47 En_346 (0) 8 : 1.000 48 En_349 (0) 8 : 1.000 49 En_121 (0) 9 : 1.000 50 En_122 (0) 9 : 1.000 51 En_125 (0) 9 : 1.000 52 En_127 (0) 9 : 1.000 53 En_128 (0) 9 : 1.000 54 En_129 (0) 9 : 1.000 55 En_306 (0) 10 : 1.000 56 En_310 (0) 10 : 1.000 57 En_312 (0) 10 : 1.000 58 En_313 (0) 10 : 1.000 59 En_317 (0) 10 : 1.000 60 En_318 (0) 10 : 1.000 61 99-45-19 (0) 11 : 1.000 62 99-45-20 (0) 11 : 1.000 63 99-45-21 (0) 11 : 1.000 64 99-45-22 (0) 11 : 1.000 65 99-45-23 (0) 11 : 1.000 66 99-45-24 (0) 11 : 1.000 67 98-123-01 (0) 12 : 1.000 68 98-123-02 (0) 12 : 1.000 69 98-123-03 (0) 12 : 1.000 70 98-123-04 (0) 12 : 1.000 71 98-123-05 (0) 12 : 1.000 72 98-123-12 (0) 12 : 1.000 73 99-93-20 (0) 13 : 1.000 74 99-93-21 (0) 13 : 1.000 75 99-93-23 (0) 13 : 1.000 76 99-93-24 (0) 13 : 1.000 77 99-93-25 (0) 13 : 1.000 78 99-93-26 (0) 13 : 1.000 79 99-21-02 (0) 14 : 1.000 80 99-21-04 (0) 14 : 1.000 81 99-21-05 (0) 14 : 1.000 82 99-21-08 (0) 14 : 1.000 83 99-21-09 (0) 14 : 1.000 84 99-21-10 (0) 14 : 1.000 85 01-58-20 (5) 15 : 1.000 86 01-58-33 (5) 15 : 1.000 87 01-58-34 (5) 15 : 1.000 88 01-58-35 (5) 15 : 1.000 89 01-58-53 (5) 15 : 1.000 90 01-58-56 (5) 15 : 1.000 91 98-116-04 (5) 16 : 1.000 92 98-116-07 (5) 16 : 1.000 93 98-116-14 (5) 16 : 1.000 94 98-116-26 (5) 16 : 1.000 95 98-116-27 (5) 16 : 1.000 Estimated Allele Frequencies in each cluster First column gives estimated ancestral frequencies Locus 1 : TAGA40 7 alleles 0.0% missing data 118 (0.590) 0.594 127 (0.072) 0.071 130 (0.077) 0.076 114 (0.031) 0.030 122 (0.092) 0.091 110 (0.077) 0.076 135 (0.062) 0.061 Locus 2 : B113 15 alleles 0.0% missing data 228 (0.097) 0.098 222 (0.116) 0.117 225 (0.154) 0.156 234 (0.015) 0.015 219 (0.140) 0.142 213 (0.217) 0.220 204 (0.011) 0.010 216 (0.035) 0.034 195 (0.016) 0.015 231 (0.025) 0.024 210 (0.025) 0.024 240 (0.011) 0.010 207 (0.020) 0.020 198 (0.106) 0.107 185 (0.011) 0.010 Locus 3 : B117 3 alleles 0.0% missing data 266 (0.848) 0.850 272 (0.032) 0.031 278 (0.120) 0.119 Locus 4 : ATG16.1 19 alleles 0.0% missing data 164 (0.104) 0.105 173 (0.305) 0.311 182 (0.067) 0.067 170 (0.020) 0.019 200 (0.020) 0.019 202 (0.010) 0.009 176 (0.010) 0.009 185 (0.025) 0.024 167 (0.039) 0.038 158 (0.067) 0.067 155 (0.029) 0.029 152 (0.052) 0.052 179 (0.011) 0.010 145 (0.011) 0.010 149 (0.053) 0.053 161 (0.057) 0.057 136 (0.100) 0.101 101 (0.010) 0.009 139 (0.010) 0.009 Locus 5 : ATG17 24 alleles 0.0% missing data 182 (0.060) 0.061 188 (0.033) 0.033 185 (0.069) 0.070 194 (0.028) 0.028 209 (0.010) 0.009 191 (0.029) 0.028 160 (0.065) 0.065 200 (0.024) 0.024 173 (0.065) 0.065 176 (0.024) 0.023 169 (0.024) 0.023 131 (0.010) 0.009 166 (0.033) 0.033 154 (0.046) 0.047 144 (0.083) 0.084 157 (0.042) 0.042 203 (0.015) 0.014 147 (0.046) 0.047 134 (0.124) 0.126 141 (0.056) 0.056 206 (0.024) 0.023 151 (0.019) 0.019 137 (0.010) 0.009 179 (0.060) 0.061 Locus 6 : ENE2 6 alleles 11.6% missing data 177 (0.166) 0.166 165 (0.149) 0.149 171 (0.424) 0.426 175 (0.161) 0.161 183 (0.053) 0.052 179 (0.047) 0.046 Locus 7 : CATG2 10 alleles 0.0% missing data 187 (0.254) 0.255 191 (0.124) 0.125 183 (0.223) 0.225 195 (0.090) 0.090 199 (0.031) 0.030 180 (0.031) 0.030 203 (0.041) 0.040 206 (0.050) 0.050 214 (0.041) 0.040 138 (0.115) 0.115 Locus 8 : ATG13 7 alleles 0.0% missing data 151 (0.556) 0.559 148 (0.046) 0.046 145 (0.121) 0.121 157 (0.011) 0.010 155 (0.077) 0.076 135 (0.026) 0.025 141 (0.162) 0.162 Locus 9 : TAGA11 10 alleles 0.0% missing data 138 (0.342) 0.345 140 (0.036) 0.035 147 (0.194) 0.195 142 (0.135) 0.135 145 (0.085) 0.085 136 (0.031) 0.030 134 (0.016) 0.015 132 (0.021) 0.020 153 (0.110) 0.110 149 (0.031) 0.030 Locus 10 : A018 7 alleles 0.0% missing data 313 (0.072) 0.071 317 (0.434) 0.436 321 (0.037) 0.036 319 (0.092) 0.092 325 (0.011) 0.010 306 (0.288) 0.289 324 (0.067) 0.066 Locus 11 : A019 8 alleles 0.0% missing data 250 (0.276) 0.278 247 (0.056) 0.056 242 (0.081) 0.081 251 (0.041) 0.040 245 (0.101) 0.101 257 (0.016) 0.015 243 (0.341) 0.343 253 (0.087) 0.086 Locus 12 : ATG26 4 alleles 0.0% missing data 204 (0.925) 0.928 180 (0.017) 0.015 218 (0.047) 0.046 210 (0.011) 0.010 Locus 13 : C111 6 alleles 0.0% missing data 260 (0.873) 0.878 263 (0.062) 0.061 257 (0.016) 0.015 269 (0.026) 0.025 275 (0.011) 0.010 246 (0.011) 0.010 Locus 14 : ENE3 5 alleles 0.0% missing data 157 (0.745) 0.749 146 (0.185) 0.185 153 (0.022) 0.021 155 (0.037) 0.036 163 (0.011) 0.010 Locus 15 : ENE4 2 alleles 0.0% missing data 243 (0.672) 0.672 238 (0.328) 0.328 Locus 16 : CATG14 3 alleles 0.0% missing data 173 (0.858) 0.860 165 (0.037) 0.036 169 (0.105) 0.104 Locus 17 : ATG18 2 alleles 0.0% missing data 171 (0.880) 0.880 168 (0.120) 0.120 Locus 18 : C114 4 alleles 0.0% missing data 286 (0.791) 0.794 287 (0.063) 0.062 283 (0.022) 0.021 290 (0.125) 0.124 Values of parameters used in structure: DATAFILE=/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/project_data, OUTFILE=/Users/jacobslab/Documents/DAE/Full_Data_Set/GobyK1ReRun/K1ReRun/Results/K1ReRun_run_1, 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=1213373734, LINKAGE=0, METROFREQ=10, REPORTHITRATE=0, MARKOVPHASE=-1, PHASED=0, PLOIDY=2, PHASEINFO=0 [STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9,