getseed(): Using stored state for mt19937b generator
Reading in data from file '../data/gaw9_d1a1-15'
1497 records of 9 columns read in
Reading in data from file '../data/gaw9_phenotyp'
1497 records of 7 columns read in
Initializing and recoding pedigree
Recoding factors
Recoding marker data
Handling data restrictions
Restriction 1: HAP1_LEFT(1),HAP1_LEFT(5),HAP1_LEFT(10),HAP1_LEFT(15),HAP1_RIGHT(1),HAP1_RIGHT(5),HAP1_RIGHT(10),HAP1_RIGHT(15)
Checking sex
Pruning pedigree
No. components = 23
No. Full Sib Families = 436
Pedigree has no loops
Processing marker 'D1G(1)' (no. alleles = 4)
Processing marker 'D1G(5)' (no. alleles = 8)
Processing marker 'D1G(10)' (no. alleles = 7)
Processing marker 'D1G(15)' (no. alleles = 4)
Processing trait locus 'QTL'
Writing out data file...
******************** Reading in data ********************

     Read 1497 records of 9 columns from '../data/gaw9_d1a1-15'
     Read 1497 records of 7 columns from '../data/gaw9_phenotyp'

******************* Recoding pedigree *******************

     No. individuals found = 1497
     No. 'dummy' parents created = 0
     Pedigree size = 1497

****************** Counting components ******************

     No. components = 23

     Component 1, size = 128, nbits = 145
     Component 2, size = 100, nbits = 110
     Component 3, size = 90, nbits = 99
     Component 4, size = 86, nbits = 100
     Component 5, size = 74, nbits = 85
     Component 6, size = 73, nbits = 83
     Component 7, size = 73, nbits = 83
     Component 8, size = 72, nbits = 72
     Component 9, size = 69, nbits = 75
     Component 10, size = 68, nbits = 73
     Component 11, size = 65, nbits = 67
     Component 12, size = 64, nbits = 62
     Component 13, size = 63, nbits = 66
     Component 14, size = 60, nbits = 63
     Component 15, size = 54, nbits = 57
     Component 16, size = 52, nbits = 56
     Component 17, size = 52, nbits = 53
     Component 18, size = 47, nbits = 49
     Component 19, size = 47, nbits = 52
     Component 20, size = 43, nbits = 47
     Component 21, size = 41, nbits = 40
     Component 22, size = 39, nbits = 42
     Component 23, size = 37, nbits = 38


******************* Family Initialization ***************

     No. Full Sib Families = 436


********************* Counting loops *********************

     Pedigree has no loops

********* Calculation of inbreeding coefficients ********

     Pedigree size = 1497

     Component 1
       Component size = 128
       Log Determinant of NRM matrix = -63.076393
       No. inbred individuals = 0
     Component 2
       Component size = 100
       Log Determinant of NRM matrix = -48.520303
       No. inbred individuals = 0
     Component 3
       Component size = 90
       Log Determinant of NRM matrix = -43.668272
       No. inbred individuals = 0
     Component 4
       Component size = 86
       Log Determinant of NRM matrix = -42.975125
       No. inbred individuals = 0
     Component 5
       Component size = 74
       Log Determinant of NRM matrix = -36.736801
       No. inbred individuals = 0
     Component 6
       Component size = 73
       Log Determinant of NRM matrix = -36.043653
       No. inbred individuals = 0
     Component 7
       Component size = 73
       Log Determinant of NRM matrix = -36.043653
       No. inbred individuals = 0
     Component 8
       Component size = 72
       Log Determinant of NRM matrix = -33.271065
       No. inbred individuals = 0
     Component 9
       Component size = 69
       Log Determinant of NRM matrix = -33.271065
       No. inbred individuals = 0
     Component 10
       Component size = 68
       Log Determinant of NRM matrix = -32.577917
       No. inbred individuals = 0
     Component 11
       Component size = 65
       Log Determinant of NRM matrix = -30.498476
       No. inbred individuals = 0
     Component 12
       Component size = 64
       Log Determinant of NRM matrix = -29.112182
       No. inbred individuals = 0
     Component 13
       Component size = 63
       Log Determinant of NRM matrix = -29.805329
       No. inbred individuals = 0
     Component 14
       Component size = 60
       Log Determinant of NRM matrix = -28.419034
       No. inbred individuals = 0
     Component 15
       Component size = 54
       Log Determinant of NRM matrix = -25.646446
       No. inbred individuals = 0
     Component 16
       Component size = 52
       Log Determinant of NRM matrix = -24.953299
       No. inbred individuals = 0
     Component 17
       Component size = 52
       Log Determinant of NRM matrix = -24.260151
       No. inbred individuals = 0
     Component 18
       Component size = 47
       Log Determinant of NRM matrix = -22.180710
       No. inbred individuals = 0
     Component 19
       Component size = 47
       Log Determinant of NRM matrix = -22.873857
       No. inbred individuals = 0
     Component 20
       Component size = 43
       Log Determinant of NRM matrix = -20.794415
       No. inbred individuals = 0
     Component 21
       Component size = 41
       Log Determinant of NRM matrix = -18.714974
       No. inbred individuals = 0
     Component 22
       Component size = 39
       Log Determinant of NRM matrix = -18.714974
       No. inbred individuals = 0
     Component 23
       Component size = 37
       Log Determinant of NRM matrix = -17.328680
       No. inbred individuals = 0

     Log Determinant of combined NRM matrix = -719.486773

*********************** Final report ********************

     Model:

       Q(1) = AGE + EF + QTL

       Name           Mean        Min      Max     No. Records
       ----           ----        ---      ---     -----------
       AGE            44.645       16       79         1000
       EF            31.2225    15.35    45.62         1000
       Q(1)          69.1616    29.16   113.02         1000


     Linkage Group - Chromosome 1:

       Marker      No. Alleles     No. Records      Het.
       ------      -----------     -----------      ----
       D1G(1)           4              1000       0.73300
       D1G(5)           8              1000       0.79900
       D1G(10)          7              1000       0.64900
       D1G(15)          4              1000       0.70400


     Marker - D1G(1):

       Allele       No. Records
       ------       -----------
        4                702
        3                663
        1                437
        2                198


     Marker - D1G(5):

       Allele       No. Records
       ------       -----------
        5                700
        4                503
        7                353
        6                183
        8                101
        1                 68
        3                 49
        2                 43


     Marker - D1G(10):

       Allele       No. Records
       ------       -----------
        6               1023
        1                487
        3                206
        2                130
        7                112
        5                 27
        4                 15


     Marker - D1G(15):

       Allele       No. Records
       ------       -----------
        4                784
        3                471
        1                360
        2                385

*********************** Exiting *************************
Reading from loki.opt
Reading from loki.dat
Reading from loki.gen
Map range for linkage group 'Chromosome 1' set to 0-60cM
Total (genome) map length set to (360,360)cM
getseed(): Using stored state for mt19937b generator
Analysis = 0
Output format: 3
Model: Q(1) = QTL + EF + AGE
Input map function: Haldane
Output map function: Haldane
Linkage groups:
  1: Chromosome 1  Map range:  (0cM to 60cM) 
    D1G(1) - 0
    D1G(5) - 8
    D1G(10) - 18
    D1G(15) - 28
Total Map Length: 360cM
Output columns:
  1: Iteration count
  2: Residual variance
  3: Total genetic variance
 covariate data:
  4: Grand mean
  5: EF effect 
  6: AGE effect 
 QTL data blocks:
  linkage group
  [position if linked]
  freq. 1
  effect 1,2
  effect 2,2
  size
Number of QTL: 0 to 5
Tau Mode: 0
Tau Beta: 160
No. fixed output columns: 6
SI_mode: 0
No. genetic groups: 1
--------------------
5 104.173 30.0501 37.0072 0.822845 0.348586 0 0.367204 2.36797 -5.92973 3.87776 0 0.307584 -11.5091 -5.45828 3.87466
10 79.3343 44.7034 32.2551 0.938422 0.315061 0 0.384988 -3.65897 -13.5553 5.50157 1 7.44456 0.643622 -1.22066 11.2143 3.79948
15 75.4842 55.2132 40.9674 0.981031 0.347751 0 0.36682 -4.08036 -15.1382 6.09826 0 0.339404 -11.9523 -11.0565 3.9199 0 0.675936 -0.286341 5.18804 1.63059
20 66.3175 72.9966 28.1646 0.983625 0.327384 0 0.350918 -6.13724 -16.9321 6.35066 0 0.688303 2.06459 15.7833 5.15402 0 0.586037 1.23138 7.016 2.47019
25 59.1409 79.168 43.4902 0.982489 0.340438 0 0.371356 -4.85656 -17.6335 6.91871 0 0.363533 -13.6598 -16.4575 5.12628 0 0.584924 0.717161 5.93628 2.2407
30 70.1256 74.1608 38.9097 0.871227 0.377544 0 0.665988 10.4456 17.2932 6.24265 0 0.323754 -16.8457 -18.9202 5.47251 1 4.39803 0.3813 -6.30795 -6.01488 2.28951
35 64.5091 77.9993 9.98744 0.99945 0.33559 0 0.595083 11.9255 16.6989 6.52407 0 0.686433 5.7688 18.8611 5.2372 1 26.2609 0.655856 0.255455 8.82414 2.82976
40 62.8178 79.2286 44.8062 0.987253 0.345224 0 0.330318 -2.28705 -14.6401 6.41456 0 0.260934 -16.2496 -20.2269 5.25783 0 0.612084 2.38895 9.93192 3.23066
45 65.2341 66.5235 55.2824 0.902332 0.359957 0 0.413825 1.55379 -9.72921 5.19423 0 0.213351 -17.7224 -22.2408 4.81717 1 3.97956 0.354436 -7.90184 -12.6509 4.04207
50 58.5417 70.3361 33.8889 0.921817 0.329892 0 0.398496 6.18176 -7.08265 6.0869 0 0.247292 -8.87526 -14.96 4.49451 1 4.33959 0.692126 4.66416 12.3442 3.61733
Dumping program state: [Parameters] [Genotypes] [Residuals] [Seed] [Time] OK
5 104.173 30.0501 37.0072 0.822845 0.348586 0 0.367204 2.36797 -5.92973 3.87776 0 0.307584 -11.5091 -5.45828 3.87466
10 79.3343 44.7034 32.2551 0.938422 0.315061 0 0.384988 -3.65897 -13.5553 5.50157 1 7.44456 0.643622 -1.22066 11.2143 3.79948
15 75.4842 55.2132 40.9674 0.981031 0.347751 0 0.36682 -4.08036 -15.1382 6.09826 0 0.339404 -11.9523 -11.0565 3.9199 0 0.675936 -0.286341 5.18804 1.63059
20 66.3175 72.9966 28.1646 0.983625 0.327384 0 0.350918 -6.13724 -16.9321 6.35066 0 0.688303 2.06459 15.7833 5.15402 0 0.586037 1.23138 7.016 2.47019
25 59.1409 79.168 43.4902 0.982489 0.340438 0 0.371356 -4.85656 -17.6335 6.91871 0 0.363533 -13.6598 -16.4575 5.12628 0 0.584924 0.717161 5.93628 2.2407
30 70.1256 74.1608 38.9097 0.871227 0.377544 0 0.665988 10.4456 17.2932 6.24265 0 0.323754 -16.8457 -18.9202 5.47251 1 4.39803 0.3813 -6.30795 -6.01488 2.28951
35 64.5091 77.9993 9.98744 0.99945 0.33559 0 0.595083 11.9255 16.6989 6.52407 0 0.686433 5.7688 18.8611 5.2372 1 26.2609 0.655856 0.255455 8.82414 2.82976
40 62.8178 79.2286 44.8062 0.987253 0.345224 0 0.330318 -2.28705 -14.6401 6.41456 0 0.260934 -16.2496 -20.2269 5.25783 0 0.612084 2.38895 9.93192 3.23066
45 65.2341 66.5235 55.2824 0.902332 0.359957 0 0.413825 1.55379 -9.72921 5.19423 0 0.213351 -17.7224 -22.2408 4.81717 1 3.97956 0.354436 -7.90184 -12.6509 4.04207
50 58.5417 70.3361 33.8889 0.921817 0.329892 0 0.398496 6.18176 -7.08265 6.0869 0 0.247292 -8.87526 -14.96 4.49451 1 4.33959 0.692126 4.66416 12.3442 3.61733
