Mercurial > repos > iuc > structureharvester
diff test-data/example_harvester_archive/Admix_run_001_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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_harvester_archive/Admix_run_001_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: 0.001 0.999 6 + 2: 0.002 0.998 6 + 3: 0.001 0.999 6 + 4: 0.002 0.998 6 + 5: 0.002 0.998 6 + 6: 0.003 0.997 6 + 7: 0.001 0.999 6 + 8: 0.001 0.999 6 + 9: 0.002 0.998 6 + 10: 0.005 0.995 6 + 11: 0.001 0.999 6 + 12: 0.002 0.998 6 + 13: 0.002 0.998 6 + 14: 0.002 0.998 6 + 15: 0.999 0.001 6 + 16: 0.998 0.002 5 +-------------------------------------------- + +Allele-freq. divergence among pops (Kullback-Leibler distance), +computed using point estimates of P. + + 1 2 + 1 - 2.67 + 2 2.10 - +-------------------------------------------- +Estimated Ln Prob of Data = -3646.5 +Mean value of ln likelihood = -3597.1 +Variance of ln likelihood = 98.8 +Mean value of alpha = 0.0254 + +Mean value of Fst_1 = 0.5120 +Mean value of Fst_2 = 0.0523 + + +Inferred ancestry of individuals: + Label (%Miss) Pop: Inferred clusters + 1 A01 (0) 1 : 0.001 0.999 + 2 A02 (0) 1 : 0.002 0.998 + 3 A03 (0) 1 : 0.001 0.999 + 4 A04 (0) 1 : 0.001 0.999 + 5 A05 (0) 1 : 0.002 0.998 + 6 A24 (0) 1 : 0.001 0.999 + 7 B466 (0) 2 : 0.001 0.999 + 8 B479 (0) 2 : 0.001 0.999 + 9 B480 (0) 2 : 0.001 0.999 + 10 B482 (0) 2 : 0.002 0.998 + 11 B484 (0) 2 : 0.003 0.997 + 12 B485 (0) 2 : 0.001 0.999 + 13 C02 (0) 3 : 0.001 0.999 + 14 C05 (0) 3 : 0.001 0.999 + 15 C14 (0) 3 : 0.001 0.999 + 16 C30 (0) 3 : 0.001 0.999 + 17 C31 (0) 3 : 0.001 0.999 + 18 C40 (0) 3 : 0.001 0.999 + 19 D08 (0) 4 : 0.002 0.998 + 20 D09 (0) 4 : 0.001 0.999 + 21 D13 (0) 4 : 0.003 0.997 + 22 D21 (0) 4 : 0.002 0.998 + 23 D25 (0) 4 : 0.001 0.999 + 24 D30 (0) 4 : 0.001 0.999 + 25 E01 (0) 5 : 0.003 0.997 + 26 E02 (0) 5 : 0.003 0.997 + 27 E03 (0) 5 : 0.001 0.999 + 28 E04 (0) 5 : 0.002 0.998 + 29 E05 (0) 5 : 0.002 0.998 + 30 E06 (0) 5 : 0.002 0.998 + 31 F03 (0) 6 : 0.010 0.990 + 32 F05 (0) 6 : 0.001 0.999 + 33 F08 (0) 6 : 0.002 0.998 + 34 F14 (0) 6 : 0.001 0.999 + 35 F25 (0) 6 : 0.001 0.999 + 36 F35 (0) 6 : 0.001 0.999 + 37 B360 (0) 7 : 0.001 0.999 + 38 B365 (0) 7 : 0.001 0.999 + 39 B367 (0) 7 : 0.001 0.999 + 40 B370 (0) 7 : 0.001 0.999 + 41 B371 (0) 7 : 0.001 0.999 + 42 B372 (0) 7 : 0.001 0.999 + 43 B341 (0) 8 : 0.002 0.998 + 44 B342 (0) 8 : 0.001 0.999 + 45 B343 (0) 8 : 0.001 0.999 + 46 B345 (0) 8 : 0.001 0.999 + 47 B346 (0) 8 : 0.001 0.999 + 48 B349 (0) 8 : 0.001 0.999 + 49 B121 (0) 9 : 0.002 0.998 + 50 B122 (0) 9 : 0.001 0.999 + 51 B125 (0) 9 : 0.003 0.997 + 52 B127 (0) 9 : 0.001 0.999 + 53 B128 (0) 9 : 0.002 0.998 + 54 B129 (0) 9 : 0.003 0.997 + 55 B306 (0) 10 : 0.016 0.984 + 56 B310 (0) 10 : 0.001 0.999 + 57 B312 (0) 10 : 0.002 0.998 + 58 B313 (0) 10 : 0.004 0.996 + 59 B317 (0) 10 : 0.001 0.999 + 60 B318 (0) 10 : 0.005 0.995 + 61 G19 (0) 11 : 0.001 0.999 + 62 G20 (0) 11 : 0.001 0.999 + 63 G21 (0) 11 : 0.001 0.999 + 64 G22 (0) 11 : 0.001 0.999 + 65 G23 (0) 11 : 0.002 0.998 + 66 G24 (0) 11 : 0.001 0.999 + 67 H01 (0) 12 : 0.001 0.999 + 68 H02 (0) 12 : 0.002 0.998 + 69 H03 (0) 12 : 0.001 0.999 + 70 H04 (0) 12 : 0.002 0.998 + 71 H05 (0) 12 : 0.002 0.998 + 72 H12 (0) 12 : 0.002 0.998 + 73 I20 (0) 13 : 0.002 0.998 + 74 I21 (0) 13 : 0.001 0.999 + 75 I23 (0) 13 : 0.002 0.998 + 76 I24 (0) 13 : 0.002 0.998 + 77 I25 (0) 13 : 0.002 0.998 + 78 I26 (0) 13 : 0.002 0.998 + 79 J02 (0) 14 : 0.002 0.998 + 80 J04 (0) 14 : 0.001 0.999 + 81 J05 (0) 14 : 0.001 0.999 + 82 J08 (0) 14 : 0.001 0.999 + 83 J09 (0) 14 : 0.002 0.998 + 84 J10 (0) 14 : 0.001 0.999 + 85 K20 (5) 15 : 0.999 0.001 + 86 K33 (5) 15 : 0.999 0.001 + 87 K34 (5) 15 : 0.999 0.001 + 88 K35 (5) 15 : 0.999 0.001 + 89 K53 (5) 15 : 0.999 0.001 + 90 K56 (5) 15 : 0.999 0.001 + 91 L04 (5) 16 : 0.999 0.001 + 92 L07 (5) 16 : 0.999 0.001 + 93 L14 (5) 16 : 0.996 0.004 + 94 L26 (5) 16 : 0.999 0.001 + 95 L27 (5) 16 : 0.999 0.001 + + +Estimated Allele Frequencies in each population +First column gives estimated ancestral frequencies + + +Locus 1 : L1 +7 alleles +0.0% missing data + 118 (0.478) 0.020 0.670 + 127 (0.104) 0.004 0.080 + 130 (0.081) 0.484 0.024 + 114 (0.069) 0.003 0.034 + 122 (0.119) 0.005 0.103 + 110 (0.107) 0.005 0.086 + 135 (0.042) 0.478 0.004 + +Locus 2 : L2 +15 alleles +0.0% missing data + 228 (0.091) 0.004 0.111 + 222 (0.099) 0.004 0.133 + 225 (0.119) 0.005 0.178 + 234 (0.043) 0.002 0.015 + 219 (0.111) 0.005 0.161 + 213 (0.147) 0.006 0.250 + 204 (0.037) 0.002 0.009 + 216 (0.058) 0.002 0.038 + 195 (0.042) 0.002 0.015 + 231 (0.052) 0.002 0.027 + 210 (0.051) 0.002 0.027 + 240 (0.037) 0.002 0.009 + 207 (0.047) 0.002 0.021 + 198 (0.034) 0.915 0.003 + 185 (0.033) 0.045 0.003 + +Locus 3 : L3 +3 alleles +0.0% missing data + 266 (0.873) 0.037 0.961 + 272 (0.079) 0.003 0.035 + 278 (0.048) 0.959 0.005 + +Locus 4 : L4 +19 alleles +0.0% missing data + 164 (0.081) 0.003 0.121 + 173 (0.146) 0.006 0.357 + 182 (0.066) 0.003 0.076 + 170 (0.043) 0.002 0.020 + 200 (0.043) 0.002 0.020 + 202 (0.034) 0.001 0.009 + 176 (0.033) 0.001 0.009 + 185 (0.045) 0.002 0.026 + 167 (0.054) 0.002 0.043 + 158 (0.067) 0.003 0.076 + 155 (0.049) 0.002 0.032 + 152 (0.061) 0.003 0.060 + 179 (0.033) 0.001 0.009 + 145 (0.034) 0.001 0.009 + 149 (0.061) 0.003 0.060 + 161 (0.063) 0.003 0.065 + 136 (0.031) 0.872 0.003 + 101 (0.029) 0.044 0.003 + 139 (0.029) 0.044 0.003 + +Locus 5 : L5 +24 alleles +0.0% missing data + 182 (0.060) 0.090 0.059 + 188 (0.040) 0.002 0.036 + 185 (0.052) 0.002 0.080 + 194 (0.038) 0.002 0.031 + 209 (0.028) 0.001 0.008 + 191 (0.038) 0.002 0.031 + 160 (0.055) 0.265 0.043 + 200 (0.036) 0.002 0.025 + 173 (0.061) 0.090 0.065 + 176 (0.036) 0.002 0.025 + 169 (0.036) 0.002 0.025 + 131 (0.028) 0.001 0.008 + 166 (0.040) 0.002 0.036 + 154 (0.045) 0.002 0.053 + 144 (0.054) 0.002 0.097 + 157 (0.044) 0.002 0.047 + 203 (0.032) 0.001 0.014 + 147 (0.044) 0.002 0.053 + 134 (0.063) 0.003 0.146 + 141 (0.047) 0.002 0.064 + 206 (0.036) 0.002 0.025 + 151 (0.035) 0.001 0.020 + 137 (0.028) 0.001 0.008 + 179 (0.024) 0.520 0.002 + +Locus 6 : L6 +6 alleles +11.6% missing data + 177 (0.168) 0.166 0.167 + 165 (0.156) 0.152 0.150 + 171 (0.346) 0.358 0.426 + 175 (0.165) 0.160 0.161 + 183 (0.086) 0.086 0.051 + 179 (0.080) 0.078 0.045 + +Locus 7 : L7 +10 alleles +0.0% missing data + 187 (0.202) 0.009 0.288 + 191 (0.125) 0.005 0.141 + 183 (0.185) 0.008 0.254 + 195 (0.105) 0.004 0.102 + 199 (0.063) 0.003 0.033 + 180 (0.063) 0.003 0.033 + 203 (0.071) 0.003 0.045 + 206 (0.078) 0.003 0.056 + 214 (0.070) 0.003 0.044 + 138 (0.039) 0.959 0.004 + +Locus 8 : L8 +7 alleles +0.0% missing data + 151 (0.466) 0.020 0.632 + 148 (0.084) 0.003 0.051 + 145 (0.059) 0.960 0.010 + 157 (0.044) 0.002 0.010 + 155 (0.109) 0.005 0.086 + 135 (0.064) 0.003 0.028 + 141 (0.174) 0.007 0.184 + +Locus 9 : L9 +10 alleles +0.0% missing data + 138 (0.241) 0.010 0.389 + 140 (0.065) 0.003 0.039 + 147 (0.137) 0.964 0.098 + 142 (0.126) 0.005 0.152 + 145 (0.098) 0.004 0.096 + 136 (0.061) 0.003 0.033 + 134 (0.047) 0.002 0.015 + 132 (0.052) 0.002 0.021 + 153 (0.112) 0.005 0.124 + 149 (0.061) 0.003 0.033 + +Locus 10 : L10 +7 alleles +0.0% missing data + 313 (0.102) 0.004 0.080 + 317 (0.368) 0.016 0.493 + 321 (0.073) 0.003 0.039 + 319 (0.109) 0.445 0.047 + 325 (0.044) 0.002 0.010 + 306 (0.262) 0.011 0.327 + 324 (0.042) 0.519 0.004 + +Locus 11 : L11 +8 alleles +0.0% missing data + 250 (0.219) 0.009 0.312 + 247 (0.083) 0.003 0.062 + 242 (0.100) 0.004 0.090 + 251 (0.072) 0.003 0.045 + 245 (0.113) 0.005 0.113 + 257 (0.049) 0.002 0.016 + 243 (0.262) 0.969 0.266 + 253 (0.104) 0.004 0.096 + +Locus 12 : L12 +4 alleles +0.0% missing data + 204 (0.823) 0.950 0.929 + 180 (0.053) 0.002 0.016 + 218 (0.085) 0.004 0.051 + 210 (0.040) 0.044 0.004 + +Locus 13 : L13 +6 alleles +0.0% missing data + 260 (0.696) 0.857 0.884 + 263 (0.111) 0.092 0.059 + 257 (0.050) 0.002 0.016 + 269 (0.061) 0.003 0.028 + 275 (0.043) 0.002 0.010 + 246 (0.038) 0.044 0.004 + +Locus 14 : L14 +5 alleles +0.0% missing data + 157 (0.640) 0.985 0.723 + 146 (0.187) 0.008 0.206 + 153 (0.057) 0.002 0.022 + 155 (0.073) 0.003 0.039 + 163 (0.043) 0.002 0.010 + +Locus 15 : L15 +2 alleles +0.0% missing data + 243 (0.639) 0.943 0.636 + 238 (0.361) 0.057 0.364 + +Locus 16 : L16 +3 alleles +0.0% missing data + 173 (0.788) 0.991 0.845 + 165 (0.077) 0.003 0.040 + 169 (0.135) 0.006 0.115 + +Locus 17 : L17 +2 alleles +0.0% missing data + 171 (0.951) 0.041 0.995 + 168 (0.049) 0.959 0.005 + +Locus 18 : L18 +4 alleles +0.0% missing data + 286 (0.764) 0.032 0.898 + 287 (0.108) 0.005 0.070 + 283 (0.064) 0.003 0.022 + 290 (0.064) 0.960 0.010 + +Values of parameters used in structure: +DATAFILE=\project_data, OUTFILE=\Results_run_2, 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