Mercurial > repos > iuc > structureharvester
diff test-data/example_harvester_archive/Admix_run_007_f @ 0:8a7390c4d6bf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
| author | iuc |
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| date | Mon, 11 Dec 2017 04:37:17 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_harvester_archive/Admix_run_007_f Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,388 @@ + + +---------------------------------------------------- +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: 0.991 0.003 0.005 0.001 6 + 2: 0.990 0.002 0.006 0.002 6 + 3: 0.995 0.001 0.002 0.001 6 + 4: 0.968 0.003 0.027 0.002 6 + 5: 0.212 0.003 0.783 0.002 6 + 6: 0.104 0.015 0.878 0.003 6 + 7: 0.991 0.002 0.006 0.001 6 + 8: 0.022 0.002 0.974 0.002 6 + 9: 0.003 0.006 0.989 0.001 6 + 10: 0.036 0.021 0.940 0.004 6 + 11: 0.002 0.988 0.009 0.001 6 + 12: 0.002 0.995 0.002 0.001 6 + 13: 0.002 0.994 0.003 0.001 6 + 14: 0.002 0.995 0.002 0.001 6 + 15: 0.001 0.001 0.001 0.997 6 + 16: 0.001 0.002 0.002 0.995 5 +-------------------------------------------- + +Allele-freq. divergence among pops (Kullback-Leibler distance), +computed using point estimates of P. + + 1 2 3 4 + 1 - 1.82 0.54 2.44 + 2 1.91 - 1.05 2.63 + 3 0.75 1.36 - 2.31 + 4 3.37 3.50 2.55 - +-------------------------------------------- +Estimated Ln Prob of Data = -2773.7 +Mean value of ln likelihood = -2678.7 +Variance of ln likelihood = 190.1 +Mean value of alpha = 0.0270 + +Mean value of Fst_1 = 0.2745 +Mean value of Fst_2 = 0.3296 +Mean value of Fst_3 = 0.1303 +Mean value of Fst_4 = 0.5180 + + +Inferred ancestry of individuals: + Label (%Miss) Pop: Inferred clusters + 1 A01 (0) 1 : 0.994 0.002 0.003 0.001 + 2 A02 (0) 1 : 0.995 0.001 0.003 0.001 + 3 A03 (0) 1 : 0.981 0.007 0.010 0.001 + 4 A04 (0) 1 : 0.995 0.002 0.002 0.001 + 5 A05 (0) 1 : 0.994 0.002 0.003 0.001 + 6 A24 (0) 1 : 0.989 0.002 0.008 0.002 + 7 B466 (0) 2 : 0.992 0.002 0.005 0.001 + 8 B479 (0) 2 : 0.995 0.001 0.003 0.001 + 9 B480 (0) 2 : 0.991 0.002 0.006 0.001 + 10 B482 (0) 2 : 0.984 0.003 0.010 0.003 + 11 B484 (0) 2 : 0.985 0.002 0.011 0.002 + 12 B485 (0) 2 : 0.993 0.002 0.004 0.001 + 13 C02 (0) 3 : 0.996 0.001 0.002 0.001 + 14 C05 (0) 3 : 0.995 0.001 0.002 0.001 + 15 C14 (0) 3 : 0.995 0.001 0.002 0.001 + 16 C30 (0) 3 : 0.995 0.002 0.002 0.001 + 17 C31 (0) 3 : 0.995 0.001 0.002 0.001 + 18 C40 (0) 3 : 0.995 0.001 0.003 0.001 + 19 D08 (0) 4 : 0.989 0.001 0.007 0.002 + 20 D09 (0) 4 : 0.990 0.002 0.006 0.001 + 21 D13 (0) 4 : 0.988 0.002 0.008 0.003 + 22 D21 (0) 4 : 0.975 0.007 0.016 0.002 + 23 D25 (0) 4 : 0.984 0.003 0.011 0.001 + 24 D30 (0) 4 : 0.881 0.004 0.114 0.001 + 25 E01 (0) 5 : 0.042 0.002 0.953 0.003 + 26 E02 (0) 5 : 0.009 0.002 0.988 0.002 + 27 E03 (0) 5 : 0.738 0.002 0.257 0.002 + 28 E04 (0) 5 : 0.332 0.002 0.664 0.002 + 29 E05 (0) 5 : 0.113 0.002 0.883 0.001 + 30 E06 (0) 5 : 0.038 0.005 0.956 0.001 + 31 F03 (0) 6 : 0.068 0.003 0.919 0.010 + 32 F05 (0) 6 : 0.040 0.011 0.948 0.001 + 33 F08 (0) 6 : 0.020 0.007 0.970 0.004 + 34 F14 (0) 6 : 0.471 0.065 0.463 0.001 + 35 F25 (0) 6 : 0.015 0.003 0.981 0.001 + 36 F35 (0) 6 : 0.010 0.002 0.987 0.001 + 37 B360 (0) 7 : 0.993 0.002 0.004 0.001 + 38 B365 (0) 7 : 0.993 0.002 0.003 0.001 + 39 B367 (0) 7 : 0.980 0.001 0.018 0.001 + 40 B370 (0) 7 : 0.994 0.002 0.003 0.001 + 41 B371 (0) 7 : 0.994 0.002 0.003 0.001 + 42 B372 (0) 7 : 0.994 0.002 0.003 0.001 + 43 B341 (0) 8 : 0.016 0.004 0.976 0.004 + 44 B342 (0) 8 : 0.065 0.002 0.932 0.001 + 45 B343 (0) 8 : 0.019 0.002 0.978 0.001 + 46 B345 (0) 8 : 0.011 0.002 0.985 0.001 + 47 B346 (0) 8 : 0.008 0.002 0.989 0.001 + 48 B349 (0) 8 : 0.012 0.002 0.985 0.001 + 49 B121 (0) 9 : 0.003 0.004 0.991 0.002 + 50 B122 (0) 9 : 0.002 0.010 0.987 0.001 + 51 B125 (0) 9 : 0.003 0.003 0.993 0.002 + 52 B127 (0) 9 : 0.003 0.003 0.993 0.001 + 53 B128 (0) 9 : 0.004 0.008 0.986 0.002 + 54 B129 (0) 9 : 0.003 0.010 0.985 0.002 + 55 B306 (0) 10 : 0.002 0.002 0.987 0.009 + 56 B310 (0) 10 : 0.002 0.023 0.973 0.001 + 57 B312 (0) 10 : 0.035 0.029 0.934 0.002 + 58 B313 (0) 10 : 0.003 0.017 0.973 0.007 + 59 B317 (0) 10 : 0.165 0.045 0.788 0.001 + 60 B318 (0) 10 : 0.006 0.007 0.985 0.002 + 61 G19 (0) 11 : 0.002 0.995 0.002 0.001 + 62 G20 (0) 11 : 0.002 0.994 0.003 0.001 + 63 G21 (0) 11 : 0.002 0.995 0.002 0.001 + 64 G22 (0) 11 : 0.003 0.959 0.037 0.001 + 65 G23 (0) 11 : 0.002 0.993 0.004 0.001 + 66 G24 (0) 11 : 0.002 0.994 0.003 0.001 + 67 H01 (0) 12 : 0.002 0.995 0.002 0.001 + 68 H02 (0) 12 : 0.001 0.995 0.003 0.001 + 69 H03 (0) 12 : 0.002 0.995 0.002 0.001 + 70 H04 (0) 12 : 0.002 0.995 0.002 0.001 + 71 H05 (0) 12 : 0.002 0.995 0.002 0.001 + 72 H12 (0) 12 : 0.001 0.996 0.002 0.001 + 73 I20 (0) 13 : 0.002 0.996 0.002 0.001 + 74 I21 (0) 13 : 0.002 0.996 0.002 0.001 + 75 I23 (0) 13 : 0.004 0.989 0.004 0.002 + 76 I24 (0) 13 : 0.002 0.995 0.002 0.001 + 77 I25 (0) 13 : 0.001 0.993 0.005 0.001 + 78 I26 (0) 13 : 0.002 0.996 0.002 0.001 + 79 J02 (0) 14 : 0.001 0.996 0.002 0.001 + 80 J04 (0) 14 : 0.002 0.995 0.002 0.001 + 81 J05 (0) 14 : 0.002 0.994 0.003 0.001 + 82 J08 (0) 14 : 0.005 0.991 0.003 0.001 + 83 J09 (0) 14 : 0.002 0.995 0.002 0.001 + 84 J10 (0) 14 : 0.001 0.996 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 : 0.001 0.006 0.004 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) 0.704 0.478 0.807 0.019 + 127 (0.086) 0.186 0.004 0.022 0.004 + 130 (0.110) 0.034 0.005 0.027 0.487 + 114 (0.083) 0.065 0.003 0.023 0.003 + 122 (0.118) 0.005 0.244 0.093 0.005 + 110 (0.085) 0.004 0.265 0.022 0.003 + 135 (0.056) 0.002 0.002 0.006 0.479 + +Locus 2 : L2 +15 alleles +0.0% missing data + 228 (0.071) 0.245 0.003 0.049 0.003 + 222 (0.112) 0.079 0.036 0.278 0.005 + 225 (0.094) 0.286 0.004 0.203 0.004 + 234 (0.056) 0.017 0.002 0.022 0.002 + 219 (0.118) 0.224 0.146 0.112 0.005 + 213 (0.122) 0.118 0.610 0.111 0.005 + 204 (0.041) 0.016 0.002 0.005 0.002 + 216 (0.065) 0.003 0.083 0.039 0.003 + 195 (0.045) 0.002 0.002 0.037 0.002 + 231 (0.049) 0.002 0.002 0.070 0.002 + 210 (0.063) 0.003 0.043 0.039 0.003 + 240 (0.042) 0.002 0.002 0.021 0.002 + 207 (0.043) 0.002 0.061 0.005 0.002 + 198 (0.040) 0.002 0.002 0.004 0.917 + 185 (0.038) 0.002 0.002 0.004 0.044 + +Locus 3 : L3 +3 alleles +0.0% missing data + 266 (0.835) 0.932 0.993 0.968 0.035 + 272 (0.098) 0.066 0.004 0.025 0.004 + 278 (0.067) 0.003 0.003 0.007 0.961 + +Locus 4 : L4 +19 alleles +0.0% missing data + 164 (0.101) 0.127 0.165 0.087 0.004 + 173 (0.104) 0.572 0.004 0.428 0.004 + 182 (0.045) 0.196 0.002 0.005 0.002 + 170 (0.054) 0.016 0.043 0.006 0.002 + 200 (0.045) 0.002 0.002 0.053 0.002 + 202 (0.040) 0.002 0.002 0.020 0.002 + 176 (0.040) 0.002 0.002 0.020 0.002 + 185 (0.042) 0.062 0.002 0.005 0.002 + 167 (0.066) 0.003 0.062 0.072 0.003 + 158 (0.073) 0.003 0.063 0.169 0.003 + 155 (0.062) 0.003 0.045 0.053 0.003 + 152 (0.055) 0.002 0.183 0.020 0.002 + 179 (0.040) 0.002 0.002 0.020 0.002 + 145 (0.041) 0.002 0.002 0.021 0.002 + 149 (0.043) 0.002 0.199 0.005 0.002 + 161 (0.042) 0.002 0.219 0.005 0.002 + 136 (0.038) 0.002 0.002 0.004 0.874 + 101 (0.036) 0.001 0.002 0.004 0.044 + 139 (0.036) 0.001 0.002 0.004 0.044 + +Locus 5 : L5 +24 alleles +0.0% missing data + 182 (0.058) 0.099 0.002 0.063 0.090 + 188 (0.032) 0.092 0.001 0.004 0.001 + 185 (0.043) 0.185 0.002 0.033 0.002 + 194 (0.041) 0.060 0.002 0.022 0.002 + 209 (0.029) 0.016 0.001 0.003 0.001 + 191 (0.044) 0.048 0.002 0.035 0.002 + 160 (0.067) 0.026 0.062 0.045 0.268 + 200 (0.040) 0.047 0.002 0.020 0.002 + 173 (0.049) 0.155 0.002 0.018 0.089 + 176 (0.040) 0.049 0.002 0.018 0.002 + 169 (0.040) 0.012 0.002 0.057 0.002 + 131 (0.029) 0.001 0.001 0.019 0.001 + 166 (0.035) 0.001 0.001 0.100 0.001 + 154 (0.047) 0.002 0.061 0.101 0.002 + 144 (0.050) 0.002 0.206 0.112 0.002 + 157 (0.045) 0.002 0.101 0.053 0.002 + 203 (0.034) 0.004 0.002 0.032 0.001 + 147 (0.047) 0.002 0.060 0.103 0.002 + 134 (0.066) 0.113 0.283 0.078 0.003 + 141 (0.044) 0.077 0.120 0.005 0.002 + 206 (0.033) 0.001 0.001 0.068 0.001 + 151 (0.030) 0.001 0.060 0.003 0.001 + 137 (0.029) 0.001 0.021 0.003 0.001 + 179 (0.028) 0.001 0.001 0.003 0.520 + +Locus 6 : L6 +6 alleles +11.6% missing data + 177 (0.216) 0.300 0.109 0.081 0.225 + 165 (0.225) 0.229 0.028 0.174 0.231 + 171 (0.340) 0.463 0.014 0.721 0.343 + 175 (0.078) 0.003 0.543 0.008 0.072 + 183 (0.071) 0.003 0.163 0.008 0.065 + 179 (0.070) 0.003 0.143 0.008 0.064 + +Locus 7 : L7 +10 alleles +0.0% missing data + 187 (0.178) 0.360 0.007 0.444 0.007 + 191 (0.118) 0.292 0.005 0.092 0.005 + 183 (0.186) 0.022 0.486 0.321 0.008 + 195 (0.066) 0.257 0.003 0.009 0.003 + 199 (0.098) 0.051 0.023 0.025 0.004 + 180 (0.085) 0.004 0.063 0.041 0.004 + 203 (0.087) 0.004 0.103 0.041 0.004 + 206 (0.074) 0.005 0.167 0.016 0.003 + 214 (0.058) 0.002 0.140 0.006 0.002 + 138 (0.051) 0.002 0.002 0.006 0.961 + +Locus 8 : L8 +7 alleles +0.0% missing data + 151 (0.402) 0.745 0.693 0.462 0.017 + 148 (0.105) 0.099 0.024 0.022 0.004 + 145 (0.078) 0.004 0.003 0.021 0.962 + 157 (0.057) 0.003 0.002 0.022 0.002 + 155 (0.122) 0.141 0.005 0.093 0.005 + 135 (0.070) 0.003 0.003 0.073 0.003 + 141 (0.164) 0.007 0.269 0.306 0.007 + +Locus 9 : L9 +10 alleles +0.0% missing data + 138 (0.194) 0.769 0.008 0.295 0.008 + 140 (0.063) 0.092 0.003 0.007 0.003 + 147 (0.140) 0.006 0.006 0.270 0.965 + 142 (0.145) 0.113 0.346 0.043 0.006 + 145 (0.132) 0.006 0.107 0.189 0.005 + 136 (0.073) 0.003 0.003 0.088 0.003 + 134 (0.062) 0.003 0.003 0.039 0.003 + 132 (0.065) 0.003 0.003 0.055 0.003 + 153 (0.066) 0.003 0.420 0.007 0.003 + 149 (0.060) 0.002 0.102 0.007 0.002 + +Locus 10 : L10 +7 alleles +0.0% missing data + 313 (0.082) 0.196 0.003 0.011 0.003 + 317 (0.331) 0.707 0.014 0.659 0.014 + 321 (0.119) 0.035 0.005 0.077 0.005 + 319 (0.170) 0.035 0.007 0.099 0.446 + 325 (0.062) 0.017 0.003 0.007 0.003 + 306 (0.174) 0.007 0.966 0.140 0.007 + 324 (0.063) 0.003 0.003 0.007 0.522 + +Locus 11 : L11 +8 alleles +0.0% missing data + 250 (0.220) 0.486 0.009 0.379 0.009 + 247 (0.070) 0.153 0.003 0.008 0.003 + 242 (0.073) 0.227 0.003 0.009 0.003 + 251 (0.112) 0.040 0.005 0.086 0.005 + 245 (0.200) 0.080 0.108 0.168 0.008 + 257 (0.066) 0.003 0.003 0.039 0.003 + 243 (0.160) 0.007 0.865 0.045 0.965 + 253 (0.099) 0.004 0.004 0.267 0.004 + +Locus 12 : L12 +4 alleles +0.0% missing data + 204 (0.818) 0.963 0.833 0.979 0.950 + 180 (0.062) 0.032 0.003 0.007 0.003 + 218 (0.065) 0.003 0.162 0.007 0.003 + 210 (0.055) 0.002 0.002 0.006 0.045 + +Locus 13 : L13 +6 alleles +0.0% missing data + 260 (0.642) 0.932 0.886 0.843 0.856 + 263 (0.138) 0.029 0.006 0.133 0.093 + 257 (0.056) 0.032 0.002 0.006 0.002 + 269 (0.058) 0.002 0.082 0.006 0.002 + 275 (0.054) 0.002 0.022 0.006 0.002 + 246 (0.051) 0.002 0.002 0.006 0.045 + +Locus 14 : L14 +5 alleles +0.0% missing data + 157 (0.586) 0.947 0.884 0.366 0.983 + 146 (0.182) 0.042 0.008 0.532 0.007 + 153 (0.072) 0.003 0.003 0.055 0.003 + 155 (0.101) 0.005 0.084 0.041 0.004 + 163 (0.059) 0.002 0.022 0.006 0.002 + +Locus 15 : L15 +2 alleles +0.0% missing data + 243 (0.697) 0.985 0.029 0.774 0.950 + 238 (0.303) 0.015 0.971 0.226 0.050 + +Locus 16 : L16 +3 alleles +0.0% missing data + 173 (0.777) 0.901 0.873 0.766 0.991 + 165 (0.068) 0.093 0.003 0.008 0.003 + 169 (0.155) 0.006 0.124 0.227 0.006 + +Locus 17 : L17 +2 alleles +0.0% missing data + 171 (0.931) 0.997 0.997 0.992 0.039 + 168 (0.069) 0.003 0.003 0.008 0.961 + +Locus 18 : L18 +4 alleles +0.0% missing data + 286 (0.738) 0.824 0.970 0.926 0.030 + 287 (0.076) 0.169 0.003 0.008 0.003 + 283 (0.097) 0.004 0.023 0.043 0.004 + 290 (0.089) 0.004 0.004 0.023 0.962 + +Values of parameters used in structure: +DATAFILE= 34\project_data, OUTFILE= \Results\DAE Admix_run_61, 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, \ No 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