Mercurial > repos > iuc > structureharvester
view test-data/example_harvester_archive/Admix_run_005_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 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: 0.001 0.997 0.002 6 2: 0.002 0.997 0.002 6 3: 0.001 0.997 0.002 6 4: 0.001 0.996 0.003 6 5: 0.002 0.995 0.003 6 6: 0.003 0.981 0.016 6 7: 0.001 0.996 0.002 6 8: 0.002 0.994 0.004 6 9: 0.002 0.960 0.038 6 10: 0.005 0.913 0.081 6 11: 0.001 0.004 0.995 6 12: 0.001 0.002 0.997 6 13: 0.001 0.002 0.996 6 14: 0.001 0.002 0.997 6 15: 0.998 0.001 0.001 6 16: 0.997 0.001 0.002 5 -------------------------------------------- Allele-freq. divergence among pops (Kullback-Leibler distance), computed using point estimates of P. 1 2 3 1 - 2.90 3.44 2 2.33 - 1.55 3 2.61 1.29 - -------------------------------------------- Estimated Ln Prob of Data = -3020.8 Mean value of ln likelihood = -2945.9 Variance of ln likelihood = 149.7 Mean value of alpha = 0.0269 Mean value of Fst_1 = 0.5216 Mean value of Fst_2 = 0.1326 Mean value of Fst_3 = 0.3273 Inferred ancestry of individuals: Label (%Miss) Pop: Inferred clusters 1 A01 (0) 1 : 0.001 0.997 0.002 2 A02 (0) 1 : 0.002 0.997 0.002 3 A03 (0) 1 : 0.001 0.997 0.002 4 A04 (0) 1 : 0.001 0.997 0.002 5 A05 (0) 1 : 0.001 0.996 0.002 6 A24 (0) 1 : 0.001 0.997 0.002 7 B466 (0) 2 : 0.001 0.997 0.002 8 B479 (0) 2 : 0.001 0.997 0.002 9 B480 (0) 2 : 0.001 0.997 0.002 10 B482 (0) 2 : 0.002 0.996 0.002 11 B484 (0) 2 : 0.002 0.996 0.002 12 B485 (0) 2 : 0.001 0.997 0.002 13 C02 (0) 3 : 0.001 0.997 0.001 14 C05 (0) 3 : 0.001 0.997 0.001 15 C14 (0) 3 : 0.002 0.997 0.001 16 C30 (0) 3 : 0.001 0.997 0.002 17 C31 (0) 3 : 0.001 0.997 0.002 18 C40 (0) 3 : 0.001 0.997 0.002 19 D08 (0) 4 : 0.001 0.997 0.001 20 D09 (0) 4 : 0.001 0.996 0.003 21 D13 (0) 4 : 0.002 0.996 0.002 22 D21 (0) 4 : 0.002 0.993 0.005 23 D25 (0) 4 : 0.001 0.996 0.003 24 D30 (0) 4 : 0.001 0.995 0.003 25 E01 (0) 5 : 0.002 0.994 0.004 26 E02 (0) 5 : 0.002 0.994 0.004 27 E03 (0) 5 : 0.002 0.996 0.002 28 E04 (0) 5 : 0.001 0.996 0.002 29 E05 (0) 5 : 0.002 0.996 0.002 30 E06 (0) 5 : 0.001 0.994 0.004 31 F03 (0) 6 : 0.012 0.985 0.003 32 F05 (0) 6 : 0.001 0.967 0.032 33 F08 (0) 6 : 0.002 0.982 0.015 34 F14 (0) 6 : 0.001 0.963 0.036 35 F25 (0) 6 : 0.001 0.994 0.005 36 F35 (0) 6 : 0.001 0.995 0.003 37 B360 (0) 7 : 0.001 0.997 0.002 38 B365 (0) 7 : 0.001 0.995 0.003 39 B367 (0) 7 : 0.001 0.997 0.002 40 B370 (0) 7 : 0.001 0.996 0.003 41 B371 (0) 7 : 0.001 0.996 0.002 42 B372 (0) 7 : 0.001 0.997 0.002 43 B341 (0) 8 : 0.008 0.984 0.008 44 B342 (0) 8 : 0.001 0.995 0.004 45 B343 (0) 8 : 0.001 0.996 0.002 46 B345 (0) 8 : 0.001 0.995 0.004 47 B346 (0) 8 : 0.001 0.997 0.002 48 B349 (0) 8 : 0.001 0.997 0.002 49 B121 (0) 9 : 0.002 0.991 0.007 50 B122 (0) 9 : 0.001 0.878 0.120 51 B125 (0) 9 : 0.002 0.993 0.005 52 B127 (0) 9 : 0.001 0.992 0.007 53 B128 (0) 9 : 0.002 0.972 0.026 54 B129 (0) 9 : 0.003 0.934 0.064 55 B306 (0) 10 : 0.015 0.974 0.010 56 B310 (0) 10 : 0.001 0.900 0.099 57 B312 (0) 10 : 0.002 0.823 0.175 58 B313 (0) 10 : 0.009 0.860 0.131 59 B317 (0) 10 : 0.001 0.943 0.055 60 B318 (0) 10 : 0.004 0.978 0.018 61 G19 (0) 11 : 0.001 0.002 0.997 62 G20 (0) 11 : 0.001 0.002 0.997 63 G21 (0) 11 : 0.001 0.002 0.997 64 G22 (0) 11 : 0.001 0.014 0.985 65 G23 (0) 11 : 0.001 0.003 0.996 66 G24 (0) 11 : 0.001 0.002 0.997 67 H01 (0) 12 : 0.001 0.002 0.997 68 H02 (0) 12 : 0.001 0.002 0.997 69 H03 (0) 12 : 0.001 0.002 0.997 70 H04 (0) 12 : 0.001 0.002 0.997 71 H05 (0) 12 : 0.001 0.002 0.997 72 H12 (0) 12 : 0.001 0.001 0.997 73 I20 (0) 13 : 0.001 0.002 0.997 74 I21 (0) 13 : 0.001 0.002 0.997 75 I23 (0) 13 : 0.002 0.004 0.993 76 I24 (0) 13 : 0.001 0.002 0.997 77 I25 (0) 13 : 0.001 0.002 0.997 78 I26 (0) 13 : 0.001 0.002 0.997 79 J02 (0) 14 : 0.001 0.002 0.997 80 J04 (0) 14 : 0.001 0.002 0.997 81 J05 (0) 14 : 0.001 0.002 0.997 82 J08 (0) 14 : 0.001 0.004 0.995 83 J09 (0) 14 : 0.001 0.002 0.997 84 J10 (0) 14 : 0.001 0.001 0.997 85 K20 (5) 15 : 0.998 0.001 0.001 86 K33 (5) 15 : 0.998 0.001 0.001 87 K34 (5) 15 : 0.998 0.001 0.001 88 K35 (5) 15 : 0.998 0.001 0.001 89 K53 (5) 15 : 0.998 0.001 0.001 90 K56 (5) 15 : 0.998 0.001 0.001 91 L04 (5) 16 : 0.998 0.001 0.001 92 L07 (5) 16 : 0.998 0.001 0.001 93 L14 (5) 16 : 0.993 0.002 0.005 94 L26 (5) 16 : 0.998 0.001 0.001 95 L27 (5) 16 : 0.998 0.001 0.001 Estimated Allele Frequencies in each population First column gives estimated ancestral frequencies Locus 1 : L1 7 alleles 0.0% missing data 118 (0.406) 0.017 0.761 0.476 127 (0.106) 0.004 0.110 0.004 130 (0.114) 0.486 0.029 0.005 114 (0.084) 0.003 0.045 0.003 122 (0.141) 0.006 0.045 0.243 110 (0.085) 0.003 0.007 0.266 135 (0.064) 0.481 0.003 0.003 Locus 2 : L2 15 alleles 0.0% missing data 228 (0.071) 0.003 0.156 0.003 222 (0.101) 0.004 0.174 0.041 225 (0.077) 0.003 0.252 0.003 234 (0.050) 0.002 0.019 0.002 219 (0.112) 0.005 0.173 0.142 213 (0.112) 0.005 0.109 0.604 204 (0.047) 0.002 0.010 0.002 216 (0.074) 0.003 0.020 0.081 195 (0.051) 0.002 0.019 0.002 231 (0.056) 0.002 0.034 0.003 210 (0.069) 0.003 0.016 0.049 240 (0.046) 0.002 0.010 0.004 207 (0.047) 0.002 0.003 0.060 198 (0.045) 0.917 0.002 0.002 185 (0.042) 0.045 0.002 0.002 Locus 3 : L3 3 alleles 0.0% missing data 266 (0.819) 0.034 0.950 0.993 272 (0.103) 0.004 0.045 0.004 278 (0.078) 0.962 0.004 0.003 Locus 4 : L4 19 alleles 0.0% missing data 164 (0.088) 0.004 0.107 0.161 173 (0.076) 0.003 0.519 0.003 182 (0.056) 0.002 0.108 0.002 170 (0.056) 0.002 0.011 0.041 200 (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 (0.049) 0.002 0.035 0.002 167 (0.069) 0.003 0.035 0.061 158 (0.079) 0.003 0.078 0.075 155 (0.063) 0.003 0.023 0.052 152 (0.052) 0.002 0.007 0.184 179 (0.042) 0.002 0.010 0.003 145 (0.041) 0.002 0.010 0.002 149 (0.044) 0.002 0.002 0.193 161 (0.045) 0.002 0.002 0.211 136 (0.038) 0.874 0.002 0.002 101 (0.037) 0.045 0.002 0.002 139 (0.038) 0.045 0.002 0.002 Locus 5 : L5 24 alleles 0.0% missing data 182 (0.051) 0.089 0.083 0.002 188 (0.038) 0.002 0.050 0.002 185 (0.040) 0.002 0.114 0.002 194 (0.037) 0.002 0.042 0.001 209 (0.031) 0.001 0.010 0.001 191 (0.037) 0.002 0.042 0.001 160 (0.064) 0.267 0.035 0.060 200 (0.035) 0.001 0.034 0.001 173 (0.051) 0.089 0.091 0.002 176 (0.036) 0.001 0.034 0.002 169 (0.035) 0.001 0.034 0.002 131 (0.031) 0.001 0.010 0.001 166 (0.037) 0.001 0.050 0.002 154 (0.052) 0.002 0.050 0.063 144 (0.054) 0.002 0.053 0.207 157 (0.050) 0.002 0.026 0.100 203 (0.034) 0.001 0.018 0.001 147 (0.051) 0.002 0.047 0.069 134 (0.057) 0.002 0.096 0.280 141 (0.052) 0.002 0.043 0.118 206 (0.035) 0.001 0.034 0.002 151 (0.032) 0.001 0.002 0.059 137 (0.030) 0.001 0.002 0.020 179 (0.029) 0.521 0.002 0.001 Locus 6 : L6 6 alleles 11.6% missing data 177 (0.259) 0.264 0.195 0.111 165 (0.218) 0.224 0.200 0.030 171 (0.264) 0.275 0.591 0.012 175 (0.092) 0.085 0.005 0.542 183 (0.084) 0.077 0.004 0.163 179 (0.082) 0.075 0.004 0.143 Locus 7 : L7 10 alleles 0.0% missing data 187 (0.129) 0.005 0.408 0.005 191 (0.103) 0.004 0.198 0.004 183 (0.178) 0.007 0.157 0.498 195 (0.095) 0.004 0.142 0.004 199 (0.099) 0.004 0.037 0.023 180 (0.095) 0.004 0.021 0.062 203 (0.096) 0.004 0.020 0.103 206 (0.084) 0.003 0.011 0.161 214 (0.063) 0.003 0.003 0.137 138 (0.057) 0.961 0.003 0.002 Locus 8 : L8 7 alleles 0.0% missing data 151 (0.366) 0.015 0.624 0.666 148 (0.120) 0.005 0.063 0.024 145 (0.084) 0.963 0.010 0.003 157 (0.061) 0.002 0.011 0.003 155 (0.102) 0.004 0.119 0.004 135 (0.078) 0.003 0.036 0.003 141 (0.188) 0.008 0.137 0.297 Locus 9 : L9 10 alleles 0.0% missing data 138 (0.147) 0.006 0.549 0.006 140 (0.077) 0.003 0.052 0.003 147 (0.151) 0.966 0.133 0.007 142 (0.144) 0.006 0.079 0.341 145 (0.140) 0.006 0.089 0.117 136 (0.075) 0.003 0.044 0.003 134 (0.064) 0.003 0.019 0.003 132 (0.070) 0.003 0.027 0.004 153 (0.069) 0.003 0.004 0.415 149 (0.063) 0.003 0.003 0.101 Locus 10 : L10 7 alleles 0.0% missing data 313 (0.127) 0.005 0.112 0.005 317 (0.263) 0.011 0.700 0.011 321 (0.103) 0.004 0.054 0.004 319 (0.163) 0.447 0.063 0.008 325 (0.071) 0.003 0.012 0.003 306 (0.199) 0.008 0.055 0.967 324 (0.073) 0.522 0.004 0.003 Locus 11 : L11 8 alleles 0.0% missing data 250 (0.166) 0.007 0.439 0.007 247 (0.101) 0.004 0.085 0.004 242 (0.111) 0.004 0.125 0.005 251 (0.092) 0.004 0.060 0.005 245 (0.174) 0.007 0.120 0.106 257 (0.071) 0.003 0.020 0.003 243 (0.170) 0.966 0.018 0.864 253 (0.115) 0.005 0.133 0.006 Locus 12 : L12 4 alleles 0.0% missing data 204 (0.789) 0.949 0.973 0.836 180 (0.074) 0.003 0.020 0.003 218 (0.075) 0.003 0.004 0.158 210 (0.062) 0.045 0.003 0.003 Locus 13 : L13 6 alleles 0.0% missing data 260 (0.621) 0.855 0.892 0.888 263 (0.129) 0.092 0.079 0.005 257 (0.067) 0.003 0.020 0.003 269 (0.065) 0.003 0.003 0.080 275 (0.060) 0.002 0.003 0.022 246 (0.057) 0.045 0.003 0.002 Locus 14 : L14 5 alleles 0.0% missing data 157 (0.608) 0.984 0.660 0.886 146 (0.144) 0.006 0.288 0.006 153 (0.077) 0.003 0.028 0.003 155 (0.109) 0.004 0.021 0.083 163 (0.063) 0.003 0.003 0.022 Locus 15 : L15 2 alleles 0.0% missing data 243 (0.627) 0.945 0.883 0.027 238 (0.373) 0.055 0.117 0.973 Locus 16 : L16 3 alleles 0.0% missing data 173 (0.730) 0.989 0.838 0.863 165 (0.092) 0.004 0.053 0.004 169 (0.179) 0.007 0.109 0.133 Locus 17 : L17 2 alleles 0.0% missing data 171 (0.919) 0.038 0.996 0.997 168 (0.081) 0.962 0.004 0.003 Locus 18 : L18 4 alleles 0.0% missing data 286 (0.672) 0.027 0.874 0.964 287 (0.120) 0.005 0.095 0.005 283 (0.110) 0.005 0.020 0.028 290 (0.099) 0.963 0.011 0.004 Values of parameters used in structure: DATAFILE= 34\project_data, OUTFILE= \Results\DAE Admix_run_54, 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,