Multivariate model
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Multivariate model
Dear ASReml-users,
For my internship at breeding cooperative Genex/CRI, Ithaca, New York as a
student of the Animal Breeding and Genetics group, Wageningen Agricultural
University, I am using ASReml to calculate BLUB EBVs for sires, using a sire
model.
I'm not sure if I should send this message to the discussion group, but this
is my 'last hope'.
The difficulty is that there are 15 linear conformation traits who need to
be analysed (as dependent variates).
I'd like to run all these 15 traits at once in one model, so I can include
the cov. matrix (15 x 15) for those 15 traits. That should be the most
accurate estimate, because you take genetic and error covariances into
account. But probably because the model becomes so big, that the model only
runs for a few traits (<15) in the model.
So my questions are:
1- a)Do you think, looking at my model (see below), that ASReml really isn't
able to run this, or should I change something in order to get the program
running?
(Memory: 4340K (1912K) real, 12908K (8780K) virtual, 371960K free)
b)Could I possibly run the program in pieces? (but still considering the
cov's?)
Everything that concerns question 1 is listed below (all the runs concern
the traits, classified within the MAP-program):
This is the .as file:
Mapscores
ROWNUMBER 12065 !I
MAPST 50 !I
MAPCW 48 !I
MAPBD 50 !I
MAPDF 49 !I
MAPRS 50 !I
MAPRW 48 !I
MAPLS 50 !I
MAPFA 50 !I
MAPFU 50 !I
MAPUH 50 !I
MAPUW 49 !I
MAPUC 50 !I
MAPUD 50 !I
MAPTP 50 !I
MAPRL 50 !I
SREG 1894 !I
MAPDIM2 59 !I
MAPAGE2 33 !I
MAPDATDHI 2585 !I
mappartcov.dat !skip 1 !BLUB 1
MAPST MAPCW MAPBD MAPDF MAPRS MAPRW MAPLS MAPFA MAPFU MAPUH MAPUW, MAPUC
MAPUD MAPTP MAPTL MAPRL ~ Trait !r Tr.SREG !f Tr.MAPDIM2 Tr.MAPDATDHI
1 2 1
0 0 0
Trait 0 US 29.36 !+2
7.06 31.53
5.34 6.33 30.20
4.57 -2.04 9.45 32.00
1.97 1.29 2.15 0.19 38.67
7.65 8.40 4.60 -0.03 -2.32 31.93
1.33 -0.12 -1.76 -1.02 -2.14 3.19 46.58
1.76 2.58 1.08 -1.05 -4.14 3.41 7.85 58.77
1.18 1.07 0.93 -1.51 -4.59 -1.19 7.19 6.69 48.81
0.72 0.75 1.88 3.17 -4.05 3.06 4.78 1.49 5.70 44.46
3.74 3.26 2.03 3.72 -3.14 4.60 5.91 2.70 5.19 23.46 40.49
-0.36 -1.85 0.70 0.62 -2.45 1.33 2.67 0.02 6.20 8.67 5.88 36.42
1.72 -1.02 -3.77 -4.13 -3.40 1.81 2.70 2.52 10.07 0.25 -1.23 6.42 38.43
-0.18 -0.79 1.94 1.54 -2.93 0.02 4.48 0.97 9.36 8.26 7.28 20.43 8.03 49.77
-3.31 -3.71 2.32 4.63 1.24 -1.37 -9.00 -3.55 -0.56 0.21 -0.41 0.25 -2.12
0.20
#estimated cov(r)
Tr.SREG
Trait 0 US 21.26 !+2
2.08 14.16
1.55 4.44 17.73
4.50 -4.76 9.13 13.05
1.81 -5.91 -4.78 0.32 19.05
1.70 4.92 2.68 -0.85 -1.17 11.22
1.95 5.31 2.82 1.02 -3.70 2.36 12.45
3.56 4.73 1.22 1.05 0.98 1.51 5.57 10.37
0 4.54 -1.50 -0.16 -2.34 -0.45 2.36 1.58 19.94
0.96 0.31 1.93 3.15 -0.73 0.56 3.67 3.08 7.98 17.29
-0.64 2.62 2.49 1.63 -1.82 3.49 3.56 2.13 6.83 12.43 12.09
1.42 0.33 -0.19 2.39 -0.38 -1.33 0.78 1.84 4.33 0.73 -0.46 19.39
6.60 1.02 -6.35 -1.26 1.18 -1.81 1.23 1.12 12.95 4.34 2.29 6.13 14.95
1.93 -0.31 -1.94 1.21 -0.18 -0.56 -1.33 1.08 5.60 1.39 -0.15 15.10 6.95
17.49
0.49 -3.27 -0.67 1.24 0.57 -1.76 -2.60 -3.05 -1.41 -2.08 -2.47 0.35 -0.20
1.10
#estimated cov(g)
SREG
- This .as file only runs with a model including only two traits.
- When I remove 'Tr.mapdatdhi' from the model, it runs untill MAPLS
(7 traits).
- When I run the full model with a small dataset (118 records, so also less
levels for 'Tr.mapdatdhi'), it runs untill MAPUW (11 traits).
The data (sample of 10 records):
ROWNUMBER MAPST MAPCW MAPBD MAPDF MAPRS MAPRW MAPLS MAPFA MAPFU MAPUH MAPUW
MAPUC MAPUD MAPTP MAPTL SREG MAPDIM2 MAPAGE2 MAPDATDHI
1 23 21 29 22 23 20 27 34 46 10 23 18 10 4 29 2079212 54 36 019441710100
2 48 15 37 28 34 26 20 25 29 33 29 42 37 28 25 2062335 23 37 059342220099
3 28 30 24 26 25 27 21 23 31 23 25 27 27 29 25 2139811 27 35 069535080206
4 28 36 34 29 20 26 24 23 23 20 20 26 24 26 23 2187617 39 35 049741200006
5 15 26 15 20 15 26 20 1 29 15 5 20 21 36 20 2109915 51 34 029935480077
6 36 38 36 35 19 36 36 19 39 35 26 39 44 46 8 2227548 53 35 099841251149
7 35 35 20 20 30 34 35 18 28 35 30 35 35 25 25 2030882 49 38 099841251149
8 20 26 38 39 20 21 35 5 20 26 28 32 20 35 29 2140608 39 32 029935480077
9 21 26 28 34 20 26 35 26 29 24 26 30 26 24 25 2113769 28 35 029935480077
10 26 25 24 26 10 12 10 5 26 26 29 35 30 39 20 1983348 29 33 029935480077
The .asr file:
ASREML [11 Jun 1999] Mapscores
Wed Jul 7 21:44:20 1999 8.00 Mbyte mapcov
QUALIFIERS: !skip 1 !BLUB 1
Reading mappartcov.dat FREE FORMAT skipping 1 lines
Multivariate analysis of MAPST MAPCW MAPBD MAPDF
Multivariate analysis of MAPRS MAPRW MAPLS MAPFA
Multivariate analysis of MAPFU MAPUH MAPUW
Using 12033 records [of 12033 read from 12033 lines of mappartcov.dat
Model term Size Type COL Minimum Mean Maximum #zero
#miss
1 ROWNUMBER 12065 Factor 1 1 6016.7407 12033 0
0
2 MAPST 50 Factor 2 1 15.3311 50 0
0
3 MAPCW 48 Factor 3 1 14.7617 48 0
0
4 MAPBD 50 Factor 4 1 13.2037 50 0
0
5 MAPDF 49 Factor 5 1 13.2500 49 0
0
6 MAPRS 50 Factor 6 1 15.5018 50 0
0
7 MAPRW 48 Factor 7 1 13.5634 48 0
0
8 MAPLS 50 Factor 8 1 16.4313 50 0
0
9 MAPFA 50 Factor 9 1 18.2212 50 0
0
10 MAPFU 50 Factor 10 1 19.0431 50 0
0
11 MAPUH 50 Factor 11 1 16.1458 50 0
0
12 MAPUW 49 Factor 12 1 13.8535 49 0
0
13 MAPUC 50 Factor 13 1 17.0631 50 0
0
14 MAPUD 50 Factor 14 1 15.2528 50 0
0
15 MAPTP 50 Factor 15 1 16.4646 50 0
0
16 MAPRL 50 Factor 16 1 14.3130 50 0
0
17 SREG 1894 Factor 17 1 450.3372 1890 0
0
18 MAPDIM2 59 Factor 18 1 28.7691 59 0
0
19 MAPAGE2 33 Factor 19 1 9.7685 33 0
0
20 MAPDATDHI 2585 Factor 20 1 1246.9348 2585 0
0
21 Trait 11 Traits/Variat
22 Tr.SREG 20834 Interaction 21 Trait : 11 17 SREG :
1894
23 Tr.MAPDIM2 649 Interaction 21 Trait : 11 18 MAPDIM2 :
59
24 Tr.MAPAGE2 363 Interaction 21 Trait : 11 19 MAPAGE2 :
33
25 Tr.MAPDATDHI28435 Interaction 21 Trait : 11 20 MAPDATDHI :
2585
Fault130665 Out of memory: forming design
mapcov.asr mappartcov.dat
Model specification: TERM LEVELS GAMMAS
Trait 11 0.00 Tr.SREG 20834 0.10 Tr.MAPDIM2 649
0.00
Tr.MAPAGE2 363 0.00 Tr.MAPDATDHI28435 0.00
SECTIONS 0 0 0
TYPE 0******** 0******** 0
25 factors define [max 500].
4440 variance parameters [max 550]. 2 special structures
Final parameter values 0.10000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000