Mercurial > repos > iuc > structureharvester
diff test-data/example_harvester_archive/Admix_run_002_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 | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_harvester_archive/Admix_run_002_f Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,384 @@ + + +---------------------------------------------------- +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, \ No newline at end of file