vendredi 28 mai 2021

Error message: Cube::init(): requested size is too large; suggest to enable ARMA_64BIT_WORD using sommer package for GWAS

Output from sessionInfo()

R version 4.0.5 (2021-03-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] sommer_4.1.4      crayon_1.4.1      lattice_0.20-41   MASS_7.3-53.1     Matrix_1.3-2      data.table_1.14.0

loaded via a namespace (and not attached):
[1] compiler_4.0.5  tools_4.0.5     rstudioapi_0.13 Rcpp_1.0.6      grid_4.0.5 

I have been trying to carry out a gwas using the sommer package with the following code:

var_cov <- A.mat(m_matrix) ## aditive relationship matrix

model <- GWAS(cbind(DW20, PLA07, PLA08, PLA09, PLA10, PLA11, PLA12, PLA13, PLA14, PLA15, PLA16, PLA17, PLA18, RGR07_09, RGR08_10, RGR09_11, RGR10_12, RGR11_13, RGR12_14, RGR13_15, RGR14_16, RGR15_17, RGR16_18, SA, SL, SW) ~ 1, random = ~ vs(accession, Gu = var_cov), data = pheno2, M = m_matrix, gTerm = "u:accession", n.PC = 5)

As described in the code, I have 26 traits and I would like to use the K+P model. My SNPs matrix has 211 260 markers and 309 accessions.

When I run this code for one and two traits, it works fine. But, when I try to run with all the 26 traits I get the error message:

Error in GWAS(cbind(DW20, PLA07, PLA08, PLA09, PLA10, PLA11, PLA12, PLA13,  : 
  Cube::init(): requested size is too large; suggest to enable ARMA_64BIT_WORD

I searched online and found that this error is related to the package RcppArmadillo. Following the suggestions here (http://arma.sourceforge.net/docs.html#config_hpp_arma_64bit_word) and here (Large Matrices in RcppArmadillo via the ARMA_64BIT_WORD define), I tried to enable the ARMA_64BIT_WORD by uncommenting the line #define ARMA_64BIT_WORD (bellow) in the file RcppArmadillo\include\armadillo_bits\config.hpp:

#if !defined(ARMA_64BIT_WORD)
//#define ARMA_64BIT_WORD 
//// Uncomment the above line if you require matrices/vectors capable of holding more than 4 billion elements.
//// Note that ARMA_64BIT_WORD is automatically enabled when std::size_t has 64 bits and ARMA_32BIT_WORD is not defined.
#endiff 

and also including the following line in the file Makevars.win in RcppArmadillo\skeleton.

PKG_CPPFLAGS = -DARMA_64BIT_WORD=1 

None of the suggestions worked and I continue getting the same error message. My questions are: is there another option to enable the ARMA_64BIT_WORD that I am missing? Is it possible to run the GWAS function in sommer package with as many traits as 26 or this number is too much? Would the error message result from a mistake in the GWAS code?

Thank you very much in advance.

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