annotate test-data/example_harvester_archive/Admix_run_005_f @ 2:28b9809c4002 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit f1cac0ad033da79288fe720fbe5af5948cc61d44

----------------------------------------------------
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,