Mercurial > repos > iuc > structureharvester
view test-data/example_harvester_archive/Admix_run_004_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 3 populations assumed 50000 Burn-in period 500000 Reps -------------------------------------------- Proportion of membership of each pre-defined population in each of the 3 clusters Given Inferred Clusters Number of Pop 1 2 3 Individuals 1: 0.002 0.997 0.001 6 2: 0.002 0.997 0.002 6 3: 0.002 0.997 0.001 6 4: 0.003 0.996 0.001 6 5: 0.003 0.995 0.002 6 6: 0.016 0.981 0.003 6 7: 0.002 0.996 0.001 6 8: 0.004 0.994 0.002 6 9: 0.038 0.961 0.002 6 10: 0.082 0.913 0.005 6 11: 0.995 0.004 0.001 6 12: 0.997 0.002 0.001 6 13: 0.997 0.002 0.001 6 14: 0.997 0.002 0.001 6 15: 0.001 0.001 0.998 6 16: 0.002 0.001 0.997 5 -------------------------------------------- Allele-freq. divergence among pops (Kullback-Leibler distance), computed using point estimates of P. 1 2 3 1 - 1.29 2.61 2 1.55 - 2.34 3 3.44 2.90 - -------------------------------------------- Estimated Ln Prob of Data = -3020.8 Mean value of ln likelihood = -2945.8 Variance of ln likelihood = 150.0 Mean value of alpha = 0.0269 Mean value of Fst_1 = 0.3266 Mean value of Fst_2 = 0.1332 Mean value of Fst_3 = 0.5223 Inferred ancestry of individuals: Label (%Miss) Pop: Inferred clusters 1 A01 (0) 1 : 0.002 0.997 0.001 2 A02 (0) 1 : 0.002 0.997 0.001 3 A03 (0) 1 : 0.002 0.997 0.001 4 A04 (0) 1 : 0.002 0.997 0.001 5 A05 (0) 1 : 0.002 0.996 0.001 6 A24 (0) 1 : 0.002 0.997 0.001 7 B466 (0) 2 : 0.002 0.997 0.001 8 B479 (0) 2 : 0.002 0.997 0.001 9 B480 (0) 2 : 0.002 0.997 0.001 10 B482 (0) 2 : 0.002 0.996 0.002 11 B484 (0) 2 : 0.002 0.996 0.002 12 B485 (0) 2 : 0.002 0.997 0.001 13 C02 (0) 3 : 0.002 0.997 0.001 14 C05 (0) 3 : 0.002 0.997 0.001 15 C14 (0) 3 : 0.001 0.997 0.001 16 C30 (0) 3 : 0.002 0.997 0.001 17 C31 (0) 3 : 0.002 0.997 0.001 18 C40 (0) 3 : 0.002 0.997 0.001 19 D08 (0) 4 : 0.001 0.997 0.001 20 D09 (0) 4 : 0.003 0.996 0.001 21 D13 (0) 4 : 0.002 0.996 0.002 22 D21 (0) 4 : 0.006 0.993 0.002 23 D25 (0) 4 : 0.003 0.996 0.001 24 D30 (0) 4 : 0.003 0.995 0.001 25 E01 (0) 5 : 0.004 0.994 0.002 26 E02 (0) 5 : 0.004 0.994 0.002 27 E03 (0) 5 : 0.003 0.996 0.001 28 E04 (0) 5 : 0.002 0.996 0.001 29 E05 (0) 5 : 0.002 0.996 0.001 30 E06 (0) 5 : 0.004 0.994 0.001 31 F03 (0) 6 : 0.003 0.985 0.012 32 F05 (0) 6 : 0.033 0.966 0.001 33 F08 (0) 6 : 0.015 0.982 0.002 34 F14 (0) 6 : 0.038 0.961 0.001 35 F25 (0) 6 : 0.005 0.994 0.001 36 F35 (0) 6 : 0.004 0.995 0.001 37 B360 (0) 7 : 0.002 0.997 0.001 38 B365 (0) 7 : 0.004 0.995 0.001 39 B367 (0) 7 : 0.002 0.997 0.001 40 B370 (0) 7 : 0.003 0.996 0.001 41 B371 (0) 7 : 0.003 0.996 0.001 42 B372 (0) 7 : 0.002 0.997 0.001 43 B341 (0) 8 : 0.008 0.985 0.007 44 B342 (0) 8 : 0.004 0.995 0.001 45 B343 (0) 8 : 0.002 0.996 0.001 46 B345 (0) 8 : 0.004 0.995 0.001 47 B346 (0) 8 : 0.002 0.997 0.001 48 B349 (0) 8 : 0.002 0.996 0.001 49 B121 (0) 9 : 0.007 0.991 0.002 50 B122 (0) 9 : 0.122 0.877 0.001 51 B125 (0) 9 : 0.005 0.993 0.002 52 B127 (0) 9 : 0.007 0.992 0.001 53 B128 (0) 9 : 0.026 0.973 0.002 54 B129 (0) 9 : 0.060 0.938 0.002 55 B306 (0) 10 : 0.011 0.974 0.015 56 B310 (0) 10 : 0.101 0.898 0.001 57 B312 (0) 10 : 0.176 0.822 0.002 58 B313 (0) 10 : 0.132 0.859 0.009 59 B317 (0) 10 : 0.053 0.945 0.001 60 B318 (0) 10 : 0.018 0.978 0.004 61 G19 (0) 11 : 0.997 0.002 0.001 62 G20 (0) 11 : 0.997 0.002 0.001 63 G21 (0) 11 : 0.997 0.002 0.001 64 G22 (0) 11 : 0.986 0.013 0.001 65 G23 (0) 11 : 0.996 0.003 0.001 66 G24 (0) 11 : 0.997 0.002 0.001 67 H01 (0) 12 : 0.997 0.002 0.001 68 H02 (0) 12 : 0.997 0.002 0.001 69 H03 (0) 12 : 0.997 0.002 0.001 70 H04 (0) 12 : 0.997 0.002 0.001 71 H05 (0) 12 : 0.997 0.002 0.001 72 H12 (0) 12 : 0.997 0.001 0.001 73 I20 (0) 13 : 0.997 0.002 0.001 74 I21 (0) 13 : 0.997 0.002 0.001 75 I23 (0) 13 : 0.993 0.004 0.002 76 I24 (0) 13 : 0.997 0.002 0.001 77 I25 (0) 13 : 0.997 0.002 0.001 78 I26 (0) 13 : 0.997 0.002 0.001 79 J02 (0) 14 : 0.997 0.002 0.001 80 J04 (0) 14 : 0.997 0.002 0.001 81 J05 (0) 14 : 0.997 0.002 0.001 82 J08 (0) 14 : 0.995 0.004 0.001 83 J09 (0) 14 : 0.997 0.002 0.001 84 J10 (0) 14 : 0.997 0.001 0.001 85 K20 (5) 15 : 0.001 0.001 0.998 86 K33 (5) 15 : 0.001 0.001 0.998 87 K34 (5) 15 : 0.001 0.001 0.998 88 K35 (5) 15 : 0.001 0.001 0.998 89 K53 (5) 15 : 0.001 0.001 0.998 90 K56 (5) 15 : 0.001 0.001 0.998 91 L04 (5) 16 : 0.001 0.001 0.998 92 L07 (5) 16 : 0.001 0.001 0.998 93 L14 (5) 16 : 0.005 0.002 0.993 94 L26 (5) 16 : 0.001 0.001 0.998 95 L27 (5) 16 : 0.001 0.001 0.998 Estimated Allele Frequencies in each population First column gives estimated ancestral frequencies Locus 1 : L1 7 alleles 0.0% missing data 118 (0.408) 0.476 0.761 0.017 127 (0.105) 0.004 0.110 0.004 130 (0.114) 0.005 0.029 0.486 114 (0.084) 0.003 0.045 0.003 122 (0.142) 0.243 0.045 0.006 110 (0.084) 0.266 0.007 0.003 135 (0.064) 0.003 0.003 0.481 Locus 2 : L2 15 alleles 0.0% missing data 228 (0.070) 0.003 0.156 0.003 222 (0.102) 0.041 0.174 0.004 225 (0.077) 0.003 0.252 0.003 234 (0.050) 0.002 0.019 0.002 219 (0.111) 0.142 0.173 0.005 213 (0.113) 0.604 0.109 0.005 204 (0.046) 0.002 0.010 0.002 216 (0.075) 0.081 0.020 0.003 195 (0.051) 0.002 0.019 0.002 231 (0.055) 0.003 0.035 0.002 210 (0.071) 0.049 0.016 0.003 240 (0.046) 0.004 0.010 0.002 207 (0.048) 0.060 0.003 0.002 198 (0.045) 0.002 0.002 0.917 185 (0.042) 0.002 0.002 0.045 Locus 3 : L3 3 alleles 0.0% missing data 266 (0.818) 0.993 0.950 0.033 272 (0.103) 0.004 0.045 0.004 278 (0.078) 0.003 0.004 0.962 Locus 4 : L4 19 alleles 0.0% missing data 164 (0.086) 0.160 0.107 0.004 173 (0.074) 0.003 0.519 0.003 182 (0.056) 0.002 0.108 0.002 170 (0.058) 0.041 0.011 0.002 200 (0.047) 0.002 0.027 0.002 202 (0.041) 0.002 0.010 0.002 176 (0.041) 0.002 0.010 0.002 185 (0.047) 0.002 0.035 0.002 167 (0.069) 0.061 0.035 0.003 158 (0.080) 0.075 0.078 0.003 155 (0.066) 0.052 0.023 0.003 152 (0.053) 0.184 0.007 0.002 179 (0.041) 0.003 0.010 0.002 145 (0.040) 0.002 0.010 0.002 149 (0.044) 0.192 0.002 0.002 161 (0.044) 0.212 0.002 0.002 136 (0.039) 0.002 0.002 0.874 101 (0.038) 0.002 0.002 0.045 139 (0.037) 0.002 0.002 0.045 Locus 5 : L5 24 alleles 0.0% missing data 182 (0.050) 0.002 0.083 0.089 188 (0.038) 0.002 0.050 0.002 185 (0.041) 0.002 0.115 0.002 194 (0.037) 0.001 0.042 0.001 209 (0.031) 0.001 0.010 0.001 191 (0.036) 0.001 0.042 0.001 160 (0.062) 0.060 0.035 0.267 200 (0.036) 0.001 0.034 0.001 173 (0.050) 0.002 0.091 0.089 176 (0.036) 0.002 0.034 0.001 169 (0.037) 0.002 0.034 0.001 131 (0.032) 0.001 0.010 0.001 166 (0.038) 0.002 0.050 0.002 154 (0.052) 0.063 0.050 0.002 144 (0.053) 0.208 0.053 0.002 157 (0.049) 0.100 0.026 0.002 203 (0.033) 0.001 0.018 0.001 147 (0.052) 0.069 0.047 0.002 134 (0.058) 0.279 0.096 0.002 141 (0.052) 0.118 0.043 0.002 206 (0.036) 0.002 0.034 0.001 151 (0.032) 0.059 0.002 0.001 137 (0.030) 0.020 0.002 0.001 179 (0.029) 0.001 0.002 0.522 Locus 6 : L6 6 alleles 11.6% missing data 177 (0.259) 0.111 0.195 0.264 165 (0.219) 0.030 0.201 0.225 171 (0.262) 0.012 0.591 0.273 175 (0.092) 0.542 0.005 0.085 183 (0.084) 0.163 0.004 0.076 179 (0.084) 0.143 0.004 0.077 Locus 7 : L7 10 alleles 0.0% missing data 187 (0.127) 0.005 0.408 0.005 191 (0.105) 0.004 0.198 0.004 183 (0.178) 0.498 0.157 0.007 195 (0.095) 0.004 0.142 0.004 199 (0.100) 0.023 0.038 0.004 180 (0.096) 0.062 0.021 0.004 203 (0.095) 0.103 0.020 0.004 206 (0.084) 0.161 0.011 0.003 214 (0.064) 0.137 0.003 0.003 138 (0.058) 0.002 0.003 0.961 Locus 8 : L8 7 alleles 0.0% missing data 151 (0.366) 0.666 0.624 0.015 148 (0.120) 0.024 0.063 0.005 145 (0.085) 0.003 0.011 0.963 157 (0.062) 0.003 0.011 0.003 155 (0.102) 0.004 0.119 0.004 135 (0.078) 0.003 0.036 0.003 141 (0.187) 0.297 0.137 0.008 Locus 9 : L9 10 alleles 0.0% missing data 138 (0.146) 0.006 0.549 0.006 140 (0.078) 0.003 0.052 0.003 147 (0.151) 0.007 0.134 0.966 142 (0.146) 0.341 0.079 0.006 145 (0.138) 0.117 0.089 0.006 136 (0.075) 0.003 0.044 0.003 134 (0.065) 0.003 0.019 0.003 132 (0.070) 0.004 0.027 0.003 153 (0.069) 0.415 0.004 0.003 149 (0.063) 0.101 0.003 0.003 Locus 10 : L10 7 alleles 0.0% missing data 313 (0.126) 0.005 0.112 0.005 317 (0.261) 0.011 0.700 0.011 321 (0.103) 0.004 0.054 0.004 319 (0.163) 0.008 0.063 0.447 325 (0.071) 0.003 0.012 0.003 306 (0.202) 0.966 0.055 0.008 324 (0.073) 0.003 0.004 0.522 Locus 11 : L11 8 alleles 0.0% missing data 250 (0.165) 0.007 0.438 0.007 247 (0.100) 0.004 0.085 0.004 242 (0.111) 0.005 0.125 0.004 251 (0.094) 0.005 0.060 0.004 245 (0.173) 0.106 0.120 0.007 257 (0.072) 0.003 0.020 0.003 243 (0.171) 0.864 0.018 0.966 253 (0.115) 0.006 0.133 0.005 Locus 12 : L12 4 alleles 0.0% missing data 204 (0.791) 0.836 0.973 0.949 180 (0.074) 0.003 0.020 0.003 218 (0.075) 0.158 0.004 0.003 210 (0.060) 0.003 0.003 0.045 Locus 13 : L13 6 alleles 0.0% missing data 260 (0.615) 0.888 0.891 0.854 263 (0.131) 0.005 0.079 0.092 257 (0.069) 0.003 0.020 0.003 269 (0.067) 0.080 0.004 0.003 275 (0.061) 0.022 0.003 0.002 246 (0.057) 0.002 0.003 0.045 Locus 14 : L14 5 alleles 0.0% missing data 157 (0.607) 0.886 0.660 0.984 146 (0.143) 0.006 0.287 0.006 153 (0.076) 0.003 0.028 0.003 155 (0.110) 0.083 0.021 0.004 163 (0.063) 0.022 0.003 0.003 Locus 15 : L15 2 alleles 0.0% missing data 243 (0.625) 0.027 0.884 0.945 238 (0.375) 0.973 0.116 0.055 Locus 16 : L16 3 alleles 0.0% missing data 173 (0.728) 0.863 0.838 0.989 165 (0.091) 0.004 0.053 0.004 169 (0.181) 0.133 0.109 0.007 Locus 17 : L17 2 alleles 0.0% missing data 171 (0.919) 0.997 0.996 0.038 168 (0.081) 0.003 0.004 0.962 Locus 18 : L18 4 alleles 0.0% missing data 286 (0.673) 0.963 0.874 0.027 287 (0.119) 0.005 0.095 0.005 283 (0.109) 0.028 0.020 0.005 290 (0.099) 0.004 0.011 0.963 Values of parameters used in structure: DATAFILE= 34\project_data, OUTFILE= \Results\DAE Admix_run_6, NUMINDS=95, NUMLOCI=18, MISSING=-9, LABEL=1, POPDATA=1, POPFLAG=0, PHENOTYPE=0, EXTRACOLS=0, MAXPOPS=3, 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,