Mercurial > repos > iuc > structureharvester
view test-data/example_harvester_archive/Admix_run_008_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 |
| parents | |
| children |
line wrap: on
line source
---------------------------------------------------- STRUCTURE by Pritchard, Stephens and Donnelly (2000) Code by J.K. Pritchard Modified by Daniel Falush to incorporate recombination breakpoints Version 2.0 (July 2001) ---------------------------------------------------- Command line arguments: bin/structure.exe -m \mainparams -e \extraparams Input File: \project_data Run parameters: 95 individuals 18 loci 4 populations assumed 50000 Burn-in period 500000 Reps -------------------------------------------- Proportion of membership of each pre-defined population in each of the 4 clusters Given Inferred Clusters Number of Pop 1 2 3 4 Individuals 1: 0.003 0.005 0.991 0.001 6 2: 0.002 0.006 0.990 0.002 6 3: 0.001 0.002 0.995 0.001 6 4: 0.003 0.027 0.968 0.002 6 5: 0.003 0.784 0.211 0.002 6 6: 0.016 0.877 0.104 0.003 6 7: 0.002 0.006 0.991 0.001 6 8: 0.003 0.974 0.021 0.002 6 9: 0.006 0.989 0.003 0.002 6 10: 0.021 0.940 0.035 0.004 6 11: 0.988 0.009 0.002 0.001 6 12: 0.995 0.002 0.002 0.001 6 13: 0.994 0.003 0.002 0.001 6 14: 0.995 0.002 0.002 0.001 6 15: 0.001 0.001 0.001 0.997 6 16: 0.002 0.002 0.001 0.995 5 -------------------------------------------- Allele-freq. divergence among pops (Kullback-Leibler distance), computed using point estimates of P. 1 2 3 4 1 - 1.05 1.91 2.62 2 1.36 - 0.74 2.31 3 1.82 0.54 - 2.44 4 3.49 2.55 3.37 - -------------------------------------------- Estimated Ln Prob of Data = -2773.4 Mean value of ln likelihood = -2678.8 Variance of ln likelihood = 189.2 Mean value of alpha = 0.0271 Mean value of Fst_1 = 0.3299 Mean value of Fst_2 = 0.1302 Mean value of Fst_3 = 0.2744 Mean value of Fst_4 = 0.5177 Inferred ancestry of individuals: Label (%Miss) Pop: Inferred clusters 1 A01 (0) 1 : 0.002 0.003 0.994 0.001 2 A02 (0) 1 : 0.001 0.003 0.995 0.001 3 A03 (0) 1 : 0.008 0.010 0.981 0.001 4 A04 (0) 1 : 0.002 0.002 0.995 0.001 5 A05 (0) 1 : 0.002 0.003 0.994 0.001 6 A24 (0) 1 : 0.002 0.007 0.989 0.002 7 B466 (0) 2 : 0.002 0.005 0.993 0.001 8 B479 (0) 2 : 0.002 0.003 0.994 0.001 9 B480 (0) 2 : 0.002 0.006 0.991 0.001 10 B482 (0) 2 : 0.003 0.009 0.985 0.003 11 B484 (0) 2 : 0.002 0.011 0.985 0.003 12 B485 (0) 2 : 0.002 0.004 0.993 0.001 13 C02 (0) 3 : 0.001 0.002 0.995 0.001 14 C05 (0) 3 : 0.001 0.002 0.995 0.001 15 C14 (0) 3 : 0.001 0.002 0.995 0.001 16 C30 (0) 3 : 0.002 0.002 0.995 0.001 17 C31 (0) 3 : 0.001 0.002 0.995 0.001 18 C40 (0) 3 : 0.002 0.003 0.995 0.001 19 D08 (0) 4 : 0.001 0.007 0.990 0.002 20 D09 (0) 4 : 0.003 0.006 0.990 0.001 21 D13 (0) 4 : 0.002 0.008 0.988 0.002 22 D21 (0) 4 : 0.007 0.015 0.976 0.002 23 D25 (0) 4 : 0.003 0.012 0.983 0.001 24 D30 (0) 4 : 0.004 0.113 0.882 0.001 25 E01 (0) 5 : 0.003 0.953 0.041 0.003 26 E02 (0) 5 : 0.003 0.988 0.008 0.001 27 E03 (0) 5 : 0.003 0.261 0.735 0.002 28 E04 (0) 5 : 0.003 0.663 0.332 0.001 29 E05 (0) 5 : 0.002 0.884 0.113 0.001 30 E06 (0) 5 : 0.005 0.957 0.037 0.001 31 F03 (0) 6 : 0.003 0.921 0.066 0.010 32 F05 (0) 6 : 0.011 0.948 0.040 0.001 33 F08 (0) 6 : 0.006 0.970 0.020 0.004 34 F14 (0) 6 : 0.069 0.458 0.472 0.001 35 F25 (0) 6 : 0.003 0.981 0.015 0.001 36 F35 (0) 6 : 0.002 0.986 0.010 0.001 37 B360 (0) 7 : 0.002 0.004 0.993 0.001 38 B365 (0) 7 : 0.002 0.003 0.993 0.001 39 B367 (0) 7 : 0.001 0.018 0.980 0.001 40 B370 (0) 7 : 0.002 0.003 0.994 0.001 41 B371 (0) 7 : 0.002 0.003 0.994 0.001 42 B372 (0) 7 : 0.002 0.003 0.994 0.001 43 B341 (0) 8 : 0.004 0.975 0.017 0.004 44 B342 (0) 8 : 0.003 0.931 0.065 0.001 45 B343 (0) 8 : 0.002 0.980 0.016 0.001 46 B345 (0) 8 : 0.003 0.986 0.010 0.001 47 B346 (0) 8 : 0.002 0.989 0.008 0.001 48 B349 (0) 8 : 0.002 0.985 0.012 0.001 49 B121 (0) 9 : 0.004 0.992 0.003 0.002 50 B122 (0) 9 : 0.010 0.986 0.002 0.001 51 B125 (0) 9 : 0.003 0.993 0.002 0.002 52 B127 (0) 9 : 0.003 0.993 0.003 0.001 53 B128 (0) 9 : 0.009 0.986 0.004 0.002 54 B129 (0) 9 : 0.010 0.985 0.003 0.002 55 B306 (0) 10 : 0.002 0.987 0.002 0.009 56 B310 (0) 10 : 0.024 0.973 0.002 0.001 57 B312 (0) 10 : 0.030 0.935 0.033 0.002 58 B313 (0) 10 : 0.017 0.973 0.003 0.007 59 B317 (0) 10 : 0.047 0.788 0.164 0.001 60 B318 (0) 10 : 0.007 0.985 0.005 0.003 61 G19 (0) 11 : 0.995 0.002 0.002 0.001 62 G20 (0) 11 : 0.995 0.002 0.002 0.001 63 G21 (0) 11 : 0.995 0.002 0.002 0.001 64 G22 (0) 11 : 0.957 0.038 0.003 0.001 65 G23 (0) 11 : 0.993 0.004 0.002 0.001 66 G24 (0) 11 : 0.994 0.003 0.002 0.001 67 H01 (0) 12 : 0.995 0.002 0.002 0.001 68 H02 (0) 12 : 0.995 0.003 0.001 0.001 69 H03 (0) 12 : 0.995 0.002 0.002 0.001 70 H04 (0) 12 : 0.995 0.002 0.002 0.001 71 H05 (0) 12 : 0.995 0.002 0.001 0.001 72 H12 (0) 12 : 0.996 0.001 0.001 0.001 73 I20 (0) 13 : 0.996 0.002 0.002 0.001 74 I21 (0) 13 : 0.996 0.002 0.002 0.001 75 I23 (0) 13 : 0.990 0.004 0.004 0.002 76 I24 (0) 13 : 0.995 0.002 0.002 0.001 77 I25 (0) 13 : 0.993 0.005 0.001 0.001 78 I26 (0) 13 : 0.996 0.002 0.002 0.001 79 J02 (0) 14 : 0.996 0.002 0.001 0.001 80 J04 (0) 14 : 0.995 0.002 0.002 0.001 81 J05 (0) 14 : 0.994 0.003 0.002 0.001 82 J08 (0) 14 : 0.992 0.003 0.004 0.001 83 J09 (0) 14 : 0.995 0.002 0.002 0.001 84 J10 (0) 14 : 0.996 0.002 0.001 0.001 85 K20 (5) 15 : 0.001 0.001 0.001 0.996 86 K33 (5) 15 : 0.001 0.001 0.001 0.997 87 K34 (5) 15 : 0.001 0.001 0.001 0.997 88 K35 (5) 15 : 0.001 0.001 0.001 0.996 89 K53 (5) 15 : 0.001 0.001 0.001 0.997 90 K56 (5) 15 : 0.001 0.001 0.001 0.997 91 L04 (5) 16 : 0.001 0.001 0.001 0.997 92 L07 (5) 16 : 0.001 0.001 0.001 0.997 93 L14 (5) 16 : 0.006 0.004 0.001 0.989 94 L26 (5) 16 : 0.001 0.001 0.001 0.996 95 L27 (5) 16 : 0.001 0.001 0.001 0.996 Estimated Allele Frequencies in each population First column gives estimated ancestral frequencies Locus 1 : L1 7 alleles 0.0% missing data 118 (0.461) 0.478 0.807 0.704 0.019 127 (0.087) 0.004 0.022 0.186 0.004 130 (0.110) 0.005 0.027 0.034 0.487 114 (0.083) 0.003 0.023 0.065 0.003 122 (0.117) 0.244 0.092 0.005 0.005 110 (0.085) 0.265 0.022 0.004 0.004 135 (0.056) 0.002 0.006 0.002 0.479 Locus 2 : L2 15 alleles 0.0% missing data 228 (0.072) 0.003 0.049 0.246 0.003 222 (0.114) 0.036 0.279 0.079 0.005 225 (0.094) 0.004 0.203 0.286 0.004 234 (0.056) 0.002 0.022 0.017 0.002 219 (0.117) 0.146 0.112 0.224 0.005 213 (0.122) 0.610 0.111 0.117 0.005 204 (0.041) 0.002 0.005 0.016 0.002 216 (0.064) 0.083 0.039 0.003 0.003 195 (0.044) 0.002 0.037 0.002 0.002 231 (0.049) 0.002 0.070 0.002 0.002 210 (0.063) 0.043 0.038 0.003 0.003 240 (0.041) 0.002 0.021 0.002 0.002 207 (0.042) 0.062 0.005 0.002 0.002 198 (0.040) 0.002 0.004 0.002 0.917 185 (0.038) 0.002 0.004 0.002 0.044 Locus 3 : L3 3 alleles 0.0% missing data 266 (0.835) 0.993 0.968 0.932 0.035 272 (0.098) 0.004 0.025 0.066 0.004 278 (0.067) 0.003 0.007 0.003 0.961 Locus 4 : L4 19 alleles 0.0% missing data 164 (0.100) 0.165 0.087 0.127 0.004 173 (0.103) 0.004 0.429 0.572 0.004 182 (0.044) 0.002 0.005 0.196 0.002 170 (0.054) 0.043 0.006 0.016 0.002 200 (0.044) 0.002 0.053 0.002 0.002 202 (0.041) 0.002 0.020 0.002 0.002 176 (0.040) 0.002 0.020 0.002 0.002 185 (0.042) 0.002 0.005 0.062 0.002 167 (0.064) 0.062 0.071 0.003 0.003 158 (0.075) 0.063 0.169 0.003 0.003 155 (0.062) 0.045 0.052 0.003 0.003 152 (0.055) 0.183 0.020 0.002 0.002 179 (0.039) 0.002 0.020 0.002 0.002 145 (0.040) 0.002 0.020 0.002 0.002 149 (0.042) 0.199 0.005 0.002 0.002 161 (0.042) 0.219 0.005 0.002 0.002 136 (0.038) 0.002 0.004 0.002 0.874 101 (0.037) 0.002 0.004 0.002 0.044 139 (0.036) 0.002 0.004 0.001 0.045 Locus 5 : L5 24 alleles 0.0% missing data 182 (0.058) 0.002 0.063 0.099 0.090 188 (0.031) 0.001 0.003 0.091 0.001 185 (0.044) 0.002 0.033 0.185 0.002 194 (0.041) 0.002 0.022 0.060 0.002 209 (0.030) 0.001 0.003 0.016 0.001 191 (0.043) 0.002 0.035 0.048 0.002 160 (0.068) 0.062 0.045 0.026 0.267 200 (0.040) 0.002 0.020 0.047 0.002 173 (0.050) 0.002 0.018 0.155 0.090 176 (0.040) 0.002 0.018 0.049 0.002 169 (0.041) 0.002 0.057 0.012 0.002 131 (0.030) 0.001 0.019 0.002 0.001 166 (0.035) 0.001 0.100 0.001 0.001 154 (0.047) 0.061 0.101 0.002 0.002 144 (0.050) 0.206 0.112 0.002 0.002 157 (0.045) 0.101 0.053 0.002 0.002 203 (0.034) 0.002 0.032 0.004 0.001 147 (0.046) 0.060 0.102 0.002 0.002 134 (0.066) 0.284 0.078 0.113 0.003 141 (0.044) 0.120 0.005 0.077 0.002 206 (0.033) 0.001 0.068 0.001 0.001 151 (0.029) 0.060 0.003 0.001 0.001 137 (0.029) 0.021 0.003 0.001 0.001 179 (0.028) 0.001 0.003 0.001 0.520 Locus 6 : L6 6 alleles 11.6% missing data 177 (0.214) 0.109 0.081 0.299 0.223 165 (0.226) 0.028 0.174 0.228 0.231 171 (0.342) 0.014 0.721 0.463 0.345 175 (0.078) 0.543 0.008 0.003 0.072 183 (0.071) 0.163 0.008 0.003 0.065 179 (0.070) 0.143 0.008 0.003 0.064 Locus 7 : L7 10 alleles 0.0% missing data 187 (0.181) 0.008 0.444 0.361 0.008 191 (0.116) 0.005 0.092 0.292 0.005 183 (0.185) 0.486 0.321 0.022 0.008 195 (0.066) 0.003 0.009 0.257 0.003 199 (0.098) 0.023 0.025 0.051 0.004 180 (0.085) 0.063 0.041 0.004 0.004 203 (0.087) 0.103 0.041 0.004 0.004 206 (0.071) 0.167 0.016 0.005 0.003 214 (0.058) 0.140 0.006 0.002 0.002 138 (0.053) 0.002 0.006 0.002 0.961 Locus 8 : L8 7 alleles 0.0% missing data 151 (0.398) 0.693 0.462 0.745 0.016 148 (0.107) 0.024 0.022 0.099 0.004 145 (0.079) 0.003 0.022 0.004 0.962 157 (0.057) 0.002 0.022 0.003 0.002 155 (0.123) 0.005 0.093 0.141 0.005 135 (0.071) 0.003 0.073 0.003 0.003 141 (0.166) 0.269 0.306 0.007 0.007 Locus 9 : L9 10 alleles 0.0% missing data 138 (0.192) 0.008 0.295 0.769 0.008 140 (0.063) 0.003 0.007 0.092 0.003 147 (0.141) 0.006 0.270 0.007 0.965 142 (0.146) 0.346 0.044 0.113 0.006 145 (0.131) 0.107 0.189 0.006 0.005 136 (0.072) 0.003 0.088 0.003 0.003 134 (0.062) 0.003 0.039 0.003 0.003 132 (0.066) 0.003 0.055 0.003 0.003 153 (0.065) 0.420 0.007 0.003 0.003 149 (0.060) 0.102 0.007 0.002 0.002 Locus 10 : L10 7 alleles 0.0% missing data 313 (0.081) 0.003 0.011 0.196 0.003 317 (0.331) 0.014 0.659 0.707 0.014 321 (0.118) 0.005 0.077 0.035 0.005 319 (0.169) 0.007 0.098 0.035 0.446 325 (0.063) 0.003 0.007 0.017 0.003 306 (0.175) 0.966 0.140 0.007 0.007 324 (0.063) 0.003 0.007 0.003 0.523 Locus 11 : L11 8 alleles 0.0% missing data 250 (0.222) 0.009 0.379 0.486 0.009 247 (0.069) 0.003 0.008 0.153 0.003 242 (0.073) 0.003 0.009 0.227 0.003 251 (0.113) 0.005 0.086 0.040 0.005 245 (0.198) 0.108 0.167 0.080 0.008 257 (0.066) 0.003 0.039 0.003 0.003 243 (0.162) 0.865 0.045 0.007 0.965 253 (0.098) 0.004 0.267 0.004 0.004 Locus 12 : L12 4 alleles 0.0% missing data 204 (0.819) 0.834 0.980 0.963 0.950 180 (0.061) 0.003 0.007 0.032 0.002 218 (0.065) 0.162 0.007 0.003 0.003 210 (0.054) 0.002 0.006 0.002 0.045 Locus 13 : L13 6 alleles 0.0% missing data 260 (0.639) 0.886 0.842 0.932 0.855 263 (0.140) 0.006 0.133 0.029 0.093 257 (0.057) 0.002 0.006 0.032 0.002 269 (0.059) 0.082 0.006 0.002 0.002 275 (0.054) 0.022 0.006 0.002 0.002 246 (0.051) 0.002 0.006 0.002 0.045 Locus 14 : L14 5 alleles 0.0% missing data 157 (0.590) 0.884 0.367 0.947 0.983 146 (0.179) 0.008 0.532 0.042 0.007 153 (0.071) 0.003 0.055 0.003 0.003 155 (0.101) 0.084 0.041 0.005 0.004 163 (0.058) 0.022 0.006 0.002 0.002 Locus 15 : L15 2 alleles 0.0% missing data 243 (0.697) 0.029 0.774 0.985 0.950 238 (0.303) 0.971 0.226 0.015 0.050 Locus 16 : L16 3 alleles 0.0% missing data 173 (0.778) 0.873 0.766 0.901 0.991 165 (0.068) 0.003 0.008 0.093 0.003 169 (0.154) 0.125 0.227 0.006 0.006 Locus 17 : L17 2 alleles 0.0% missing data 171 (0.931) 0.997 0.992 0.997 0.039 168 (0.069) 0.003 0.008 0.003 0.961 Locus 18 : L18 4 alleles 0.0% missing data 286 (0.737) 0.970 0.926 0.824 0.030 287 (0.076) 0.003 0.008 0.169 0.003 283 (0.097) 0.023 0.043 0.004 0.004 290 (0.090) 0.004 0.023 0.004 0.962 Values of parameters used in structure: DATAFILE= 34\project_data, OUTFILE= \Results\DAE Admix_run_66, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=4, 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 [STRAT parameters]: NUMSIMSTATS=1000, PHENOTYPECOL=-9, POOLFREQ=10, LOCUSxONLY=0, EMERROR=0.00100, MISSINGPHENO=-9,