readme.pcg2
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readme.pcg2 [2012/05/28 14:37] – shogo | readme.pcg2 [2022/05/09 17:53] – [Storing solutions with original ID] dani | ||
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+ | ====== BLUP90IOD2 ====== | ||
- | Available options: | + | ===== Summary ===== |
+ | The original program was written by Shogo Tsuruta in 1999. | ||
+ | \\ | ||
+ | BLUP90IOD2 is a BLUP program for solving a large number of mixed model equations, using preconditioned conjugate gradient (PCG). Another version for heterogeneous residual variances is also available. | ||
+ | \\ | ||
+ | BLUP90IOD2 has 2 additional versions: BLUP90IOD2OMP1 with OpenMP and BLUP90IOD2MPI with MPI. The OpenMP version is faster running with multiple cores. The MPI version has the same computing speed as the OpenMP version with less memory when we use SSD. | ||
+ | \\ | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
+ | \\ | ||
+ | Implementation of one-step genomic selection updating animal effects with the combined pedigree and genomic relationship matrix (H-Inverse). | ||
+ | ====== Options ====== | ||
+ | < | ||
OPTION conv_crit 1e-12 | OPTION conv_crit 1e-12 | ||
- | + | </ | |
- | Set convergence | + | Set a convergence |
+ | < | ||
OPTION maxrounds 10000 | OPTION maxrounds 10000 | ||
- | + | </ | |
- | Set maximum number of rounds (default | + | Set maximum number of rounds (default |
+ | < | ||
OPTION blksize 3 | OPTION blksize 3 | ||
- | + | </ | |
- | Set block size for preconditioner (default 1). | + | Set a block size for preconditioner (default 1) to accelerate convergence (usually 2 to 5 times faster). For a multiple-trait model, use the number of traits. |
+ | < | ||
OPTION init_eq 10 | OPTION init_eq 10 | ||
- | | + | </ |
+ | Set the number of effects to be solved directly (default=0) | ||
+ | < | ||
+ | OPTION solv_method FSPAK | ||
+ | </ | ||
+ | Solving method for initial equations (default=DIRECT). | ||
+ | < | ||
+ | OPTION tol 1d-12 | ||
+ | </ | ||
+ | Tolerance to get a positive definite covariance component matrix (default=1d-12). | ||
+ | < | ||
+ | OPTION residual | ||
+ | </ | ||
+ | y-hat and residuals will be included in " | ||
+ | < | ||
+ | OPTION avgeps 50 | ||
+ | </ | ||
+ | Using the last 50 average eps for convergence, | ||
+ | < | ||
OPTION cont 1 | OPTION cont 1 | ||
- | | + | </ |
- | + | To restart the program from the last solutions. | |
- | OPTION missing -1 | + | < |
- | set the missing value (default 0). | + | OPTION missing -999 |
+ | </ | ||
+ | Set the missing value (default 0) in integer. | ||
+ | < | ||
OPTION restart 100 | OPTION restart 100 | ||
- | | + | </ |
+ | Set the number of iteration to recompute residuals (default=100). | ||
+ | < | ||
+ | OPTION prior_solutions | ||
+ | </ | ||
+ | Using the previous solution file to start the iteration. An additional software is required to use this option. | ||
+ | < | ||
+ | OPTION random_upg 1 2 | ||
+ | </ | ||
+ | Set the UPG random. " | ||
+ | < | ||
+ | OPTION SNP_file snp | ||
+ | </ | ||
+ | Specify the SNP file name to use genotype data. \\ | ||
+ | \\ | ||
+ | ==== Storing solutions with original ID ==== | ||
+ | blup90iod2 allows storing solutions with original ID. To do it, simply add the following option: | ||
+ | OPTION origID | ||
+ | The output is //trait effect level original_id solution//, and is stored in '' | ||
- | OPTION SNP_file snps | ||
- | | ||
- | For information on availability of BLUP90IOD, please contact Ignacy | ||
- | Misztal (ignacy@uga.edu) at the University of Georgia. | ||
readme.pcg2.txt · Last modified: 2024/05/16 14:16 by dani