Mercurial > repos > iuc > structureharvester
diff test-data/example_harvester_archive/K1ReRun_run_1_f @ 0:8a7390c4d6bf draft
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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_harvester_archive/K1ReRun_run_1_f Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,384 @@ + + +---------------------------------------------------- +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, \ No newline at end of file