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  ASReml  ~  Bivariate genetic model processing issues

Guspaixao
Posted: Mon May 14, 2018 12:23 pm Reply with quote
Joined: 10 Apr 2018 Posts: 1
Dear all,

I am running a bivariate genetic analysis on reproduction traits, but the computation process is taking more than I expected. The last run proceeded for over 72h (when I finally aborted the job) without converging.
When I try to simplify the model, taking out one random effect - PERM (and changing the .pin file accordingly), the model seems to work, with plausible results, but it takes a while to compute also. Notwithstanding, I do want to include the PERM effect to calculate the proportion of non-genetic permanent effects, and ideally, I would like to run the 4 traits together, instead of 2.
Should I increase the workspace? Limit the estimates?

I am running on ASREML 4, 64bits, Windows 10, 8GB ram.

All the help would be much appreciated.

.as file:
ID !P # 219701 individuals in the pedigree file
PERM !I # 10988 animals
HY !A 801
SEASON !A 4
AGE
AGEQ
NBT
NBA
bisgen.ped
bis_BD.txt !skip 1 !WORKSPACE 12000
NBT NBA ~ Trait Trait.HY Trait.SEASON !r us(Trait).id(ID) us(Trait).id(PERM) !f Trait.AGE Trait.AGEQ
residual id(units).us(Trait !GPFP)
VPREDICT

.pin file:
F phenvar 1:3 + 4:6 + 7:9 #10 11 12
F animalA 7 * 1 #13
F animalB 9 * 1 #14
F perm_genA 4 * 1 #15
F perm_genB 7 * 1 # 16
H heritA 13 10
H heritB 14 12
H RepA 15 10
H RepB 16 12
R phencorr 10 11 12
R gencorr 7:9

Kind regards,
Gustavo Paix„o
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Arthur
Posted: Tue May 15, 2018 12:01 pm Reply with quote
Joined: 05 Aug 2008 Posts: 471 Location: Orange, NSW
Dear Gustavo,

I really need to see the outputs to comment properly.
You can send them me directly and I can review what you are doing.
However, I am currently travelling so have little opportunity for running such big jobs.
But I could comment on whether the time and convergence is as I would expect.

Email your .asr file to arthur@vsni.co.uk

_________________
Arthur Gilmour

Retired Principal Research Scientist (Biometrics)
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