Mercurial > repos > iuc > structureharvester
view test-data/example_harvester_archive/Admix_run_002_f @ 2:28b9809c4002 draft default tip
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 |
| 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 2 populations assumed 50000 Burn-in period 500000 Reps -------------------------------------------- Proportion of membership of each pre-defined population in each of the 2 clusters Given Inferred Clusters Number of Pop 1 2 Individuals 1: 0.006 0.994 6 2: 0.005 0.995 6 3: 0.004 0.996 6 4: 0.015 0.985 6 5: 0.013 0.987 6 6: 0.091 0.909 6 7: 0.007 0.993 6 8: 0.024 0.976 6 9: 0.638 0.362 6 10: 0.485 0.515 6 11: 0.995 0.005 6 12: 0.996 0.004 6 13: 0.996 0.004 6 14: 0.995 0.005 6 15: 0.004 0.996 6 16: 0.005 0.995 5 -------------------------------------------- Allele-freq. divergence among pops (Kullback-Leibler distance), computed using point estimates of P. 1 2 1 - 1.44 2 1.50 - -------------------------------------------- Estimated Ln Prob of Data = -3631.9 Mean value of ln likelihood = -3562.2 Variance of ln likelihood = 139.5 Mean value of alpha = 0.0695 Mean value of Fst_1 = 0.2830 Mean value of Fst_2 = 0.1203 Inferred ancestry of individuals: Label (%Miss) Pop: Inferred clusters 1 A01 (0) 1 : 0.005 0.995 2 A02 (0) 1 : 0.005 0.995 3 A03 (0) 1 : 0.009 0.991 4 A04 (0) 1 : 0.005 0.995 5 A05 (0) 1 : 0.006 0.994 6 A24 (0) 1 : 0.005 0.995 7 B466 (0) 2 : 0.005 0.995 8 B479 (0) 2 : 0.005 0.995 9 B480 (0) 2 : 0.005 0.995 10 B482 (0) 2 : 0.006 0.994 11 B484 (0) 2 : 0.004 0.996 12 B485 (0) 2 : 0.006 0.994 13 C02 (0) 3 : 0.004 0.996 14 C05 (0) 3 : 0.004 0.996 15 C14 (0) 3 : 0.004 0.996 16 C30 (0) 3 : 0.005 0.995 17 C31 (0) 3 : 0.004 0.996 18 C40 (0) 3 : 0.004 0.996 19 D08 (0) 4 : 0.004 0.996 20 D09 (0) 4 : 0.011 0.989 21 D13 (0) 4 : 0.007 0.993 22 D21 (0) 4 : 0.016 0.984 23 D25 (0) 4 : 0.014 0.986 24 D30 (0) 4 : 0.037 0.963 25 E01 (0) 5 : 0.017 0.983 26 E02 (0) 5 : 0.019 0.981 27 E03 (0) 5 : 0.006 0.994 28 E04 (0) 5 : 0.009 0.991 29 E05 (0) 5 : 0.006 0.994 30 E06 (0) 5 : 0.019 0.981 31 F03 (0) 6 : 0.009 0.991 32 F05 (0) 6 : 0.185 0.815 33 F08 (0) 6 : 0.095 0.905 34 F14 (0) 6 : 0.155 0.845 35 F25 (0) 6 : 0.023 0.977 36 F35 (0) 6 : 0.081 0.919 37 B360 (0) 7 : 0.006 0.994 38 B365 (0) 7 : 0.010 0.990 39 B367 (0) 7 : 0.005 0.995 40 B370 (0) 7 : 0.007 0.993 41 B371 (0) 7 : 0.008 0.992 42 B372 (0) 7 : 0.007 0.993 43 B341 (0) 8 : 0.008 0.992 44 B342 (0) 8 : 0.019 0.981 45 B343 (0) 8 : 0.014 0.986 46 B345 (0) 8 : 0.075 0.925 47 B346 (0) 8 : 0.009 0.991 48 B349 (0) 8 : 0.019 0.981 49 B121 (0) 9 : 0.439 0.561 50 B122 (0) 9 : 0.885 0.115 51 B125 (0) 9 : 0.452 0.548 52 B127 (0) 9 : 0.751 0.249 53 B128 (0) 9 : 0.651 0.349 54 B129 (0) 9 : 0.650 0.350 55 B306 (0) 10 : 0.407 0.593 56 B310 (0) 10 : 0.554 0.446 57 B312 (0) 10 : 0.542 0.458 58 B313 (0) 10 : 0.541 0.459 59 B317 (0) 10 : 0.427 0.573 60 B318 (0) 10 : 0.435 0.565 61 G19 (0) 11 : 0.996 0.004 62 G20 (0) 11 : 0.995 0.005 63 G21 (0) 11 : 0.996 0.004 64 G22 (0) 11 : 0.993 0.007 65 G23 (0) 11 : 0.995 0.005 66 G24 (0) 11 : 0.995 0.005 67 H01 (0) 12 : 0.995 0.005 68 H02 (0) 12 : 0.996 0.004 69 H03 (0) 12 : 0.996 0.004 70 H04 (0) 12 : 0.996 0.004 71 H05 (0) 12 : 0.996 0.004 72 H12 (0) 12 : 0.997 0.003 73 I20 (0) 13 : 0.996 0.004 74 I21 (0) 13 : 0.996 0.004 75 I23 (0) 13 : 0.994 0.006 76 I24 (0) 13 : 0.996 0.004 77 I25 (0) 13 : 0.996 0.004 78 I26 (0) 13 : 0.996 0.004 79 J02 (0) 14 : 0.996 0.004 80 J04 (0) 14 : 0.995 0.005 81 J05 (0) 14 : 0.995 0.005 82 J08 (0) 14 : 0.992 0.008 83 J09 (0) 14 : 0.996 0.004 84 J10 (0) 14 : 0.997 0.003 85 K20 (5) 15 : 0.004 0.996 86 K33 (5) 15 : 0.004 0.996 87 K34 (5) 15 : 0.004 0.996 88 K35 (5) 15 : 0.004 0.996 89 K53 (5) 15 : 0.004 0.996 90 K56 (5) 15 : 0.004 0.996 91 L04 (5) 16 : 0.004 0.996 92 L07 (5) 16 : 0.004 0.996 93 L14 (5) 16 : 0.007 0.993 94 L26 (5) 16 : 0.004 0.996 95 L27 (5) 16 : 0.004 0.996 Estimated Allele Frequencies in each population First column gives estimated ancestral frequencies Locus 1 : L1 7 alleles 0.0% missing data 118 (0.436) 0.552 0.626 127 (0.098) 0.004 0.103 130 (0.102) 0.004 0.110 114 (0.077) 0.003 0.042 122 (0.123) 0.219 0.028 110 (0.069) 0.214 0.004 135 (0.094) 0.004 0.087 Locus 2 : L2 15 alleles 0.0% missing data 228 (0.071) 0.004 0.146 222 (0.114) 0.076 0.142 225 (0.082) 0.004 0.236 234 (0.048) 0.002 0.017 219 (0.118) 0.118 0.160 213 (0.112) 0.548 0.065 204 (0.042) 0.002 0.010 216 (0.073) 0.065 0.018 195 (0.047) 0.002 0.017 231 (0.046) 0.059 0.004 210 (0.048) 0.060 0.004 240 (0.042) 0.008 0.006 207 (0.044) 0.047 0.002 198 (0.073) 0.003 0.161 185 (0.042) 0.002 0.010 Locus 3 : L3 3 alleles 0.0% missing data 266 (0.766) 0.991 0.784 272 (0.090) 0.004 0.042 278 (0.144) 0.006 0.174 Locus 4 : L4 19 alleles 0.0% missing data 164 (0.100) 0.155 0.085 173 (0.091) 0.003 0.505 182 (0.061) 0.002 0.105 170 (0.061) 0.031 0.011 200 (0.048) 0.002 0.026 202 (0.040) 0.003 0.009 176 (0.041) 0.002 0.010 185 (0.050) 0.002 0.034 167 (0.046) 0.097 0.004 158 (0.051) 0.178 0.005 155 (0.045) 0.069 0.004 152 (0.045) 0.140 0.003 179 (0.040) 0.008 0.007 145 (0.040) 0.006 0.008 149 (0.045) 0.141 0.003 161 (0.045) 0.155 0.003 136 (0.068) 0.002 0.160 101 (0.040) 0.002 0.010 139 (0.041) 0.002 0.010 Locus 5 : L5 24 alleles 0.0% missing data 182 (0.041) 0.002 0.097 188 (0.038) 0.001 0.049 185 (0.041) 0.002 0.113 194 (0.037) 0.001 0.042 209 (0.030) 0.001 0.010 191 (0.038) 0.001 0.042 160 (0.061) 0.043 0.082 200 (0.036) 0.001 0.034 173 (0.042) 0.002 0.105 176 (0.037) 0.002 0.033 169 (0.043) 0.034 0.015 131 (0.030) 0.001 0.010 166 (0.037) 0.001 0.049 154 (0.056) 0.054 0.044 144 (0.046) 0.212 0.015 157 (0.050) 0.081 0.020 203 (0.035) 0.006 0.015 147 (0.042) 0.113 0.009 134 (0.065) 0.248 0.068 141 (0.058) 0.085 0.042 206 (0.034) 0.050 0.005 151 (0.031) 0.042 0.002 137 (0.030) 0.015 0.002 179 (0.041) 0.001 0.097 Locus 6 : L6 6 alleles 11.6% missing data 177 (0.234) 0.104 0.202 165 (0.202) 0.052 0.198 171 (0.337) 0.089 0.586 175 (0.082) 0.482 0.005 183 (0.073) 0.145 0.004 179 (0.072) 0.127 0.004 Locus 7 : L7 10 alleles 0.0% missing data 187 (0.145) 0.012 0.372 191 (0.106) 0.005 0.182 183 (0.160) 0.556 0.074 195 (0.094) 0.004 0.130 199 (0.095) 0.019 0.035 180 (0.091) 0.053 0.019 203 (0.081) 0.096 0.012 206 (0.069) 0.139 0.006 214 (0.058) 0.112 0.003 138 (0.101) 0.004 0.167 Locus 8 : L8 7 alleles 0.0% missing data 151 (0.437) 0.502 0.605 148 (0.121) 0.020 0.061 145 (0.122) 0.004 0.188 157 (0.056) 0.004 0.010 155 (0.105) 0.004 0.116 135 (0.075) 0.043 0.012 141 (0.084) 0.423 0.007 Locus 9 : L9 10 alleles 0.0% missing data 138 (0.172) 0.011 0.496 140 (0.076) 0.003 0.047 147 (0.150) 0.019 0.275 142 (0.155) 0.291 0.071 145 (0.124) 0.200 0.037 136 (0.072) 0.003 0.040 134 (0.060) 0.003 0.017 132 (0.066) 0.036 0.010 153 (0.067) 0.350 0.004 149 (0.059) 0.085 0.003 Locus 10 : L10 7 alleles 0.0% missing data 313 (0.122) 0.005 0.100 317 (0.357) 0.047 0.617 321 (0.098) 0.005 0.048 319 (0.146) 0.013 0.127 325 (0.064) 0.003 0.011 306 (0.096) 0.921 0.005 324 (0.118) 0.005 0.093 Locus 11 : L11 8 alleles 0.0% missing data 250 (0.164) 0.008 0.418 247 (0.090) 0.003 0.081 242 (0.100) 0.004 0.120 251 (0.092) 0.013 0.053 245 (0.162) 0.087 0.112 257 (0.063) 0.003 0.019 243 (0.249) 0.655 0.188 253 (0.080) 0.228 0.009 Locus 12 : L12 4 alleles 0.0% missing data 204 (0.795) 0.869 0.966 180 (0.070) 0.003 0.019 218 (0.073) 0.126 0.004 210 (0.061) 0.002 0.011 Locus 13 : L13 6 alleles 0.0% missing data 260 (0.654) 0.910 0.876 263 (0.100) 0.004 0.088 257 (0.066) 0.003 0.019 269 (0.064) 0.063 0.004 275 (0.058) 0.017 0.003 246 (0.058) 0.002 0.011 Locus 14 : L14 5 alleles 0.0% missing data 157 (0.592) 0.892 0.692 146 (0.170) 0.015 0.260 153 (0.073) 0.003 0.026 155 (0.107) 0.071 0.019 163 (0.058) 0.018 0.003 Locus 15 : L15 2 alleles 0.0% missing data 243 (0.690) 0.101 0.918 238 (0.310) 0.899 0.082 Locus 16 : L16 3 alleles 0.0% missing data 173 (0.737) 0.805 0.891 165 (0.090) 0.004 0.050 169 (0.173) 0.191 0.059 Locus 17 : L17 2 alleles 0.0% missing data 171 (0.850) 0.994 0.826 168 (0.150) 0.006 0.174 Locus 18 : L18 4 alleles 0.0% missing data 286 (0.676) 0.949 0.722 287 (0.108) 0.004 0.089 283 (0.076) 0.042 0.007 290 (0.140) 0.006 0.182 Values of parameters used in structure: DATAFILE=\project_data, OUTFILE=\Results_run_3, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=2, 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,