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--- readme.pcgtest [2023/08/24 22:23] – andres
+++ readme.pcgtest [2024/03/07 22:28] – [Tips for running BLUP90IOD3] shogo
@@ Line 14: / Line 14: @@
 OPTION conv_crit 1e-12
 </file>
-Set convergence criteria (deault 1e-12).
+Set convergence criteria (default 1e-12).
+For single-trait models, it may be better to use < 1e-12 (e.g., 1e-14, 1e-16).
+For multi-trait models, usually, 1e-12 is enough.
 <file>
 OPTION maxrounds 10000
 </file>
 Set maximum number of rounds (default 1000).
+If the program does not converge with many rounds, it is would be better to reconsider the model, (co)variance components, the data used.
 <file>
-OPTION blksize 3
+OPTION blksize n
 </file>
-Set block size for preconditioner (default 1).
+Set block size for preconditioner (default n=1), e.g. the preconditioner is the inverse of a block diagonal matrix.
+For a model with multiple trait  with n traits  it is recommended to use ''OPTION blksize n''. E.g for three traits ''OPTION blksize 3'' .
+For a model with a single trait but correlated random effects such as maternal effect models, random regression models, "OPTION blksize x cor" could make convergence faster.
+For the case of a multiple trait model with correlated random effects use ''OPTION blksize n'' with n number of traits.
 <file>
 OPTION init_eq 10
@@ Line 42: / Line 51: @@
 OPTION avgeps 50
 </file>
-Using the last 50 average eps for convergence.
+Using the last 50 average eps for convergence. This is useful when the iteration is largely fluctuated. With this option, the "conv_crit" value can be larger (e.g., 1e-10).
 <file>
 OPTION cont 1
@@ Line 50: / Line 59: @@
 OPTION missing -999
 </file>
-Set the missing value (default 0) in integer.
+Set the missing value (default 0) in integer. "-999" can be any integer number.
 <file>
 OPTION restart 100
@@ Line 62: / Line 71: @@
 OPTION random_upg
 </file>
-Set the UPG random.
+Set the UPG random. When numbers of animals in UPG are small (e.g., < 100 or < 1000), this option can predict UPG effects stably as random instead of fixed.
 <file>
 OPTION SNP_file snp
@@ Line 71: / Line 80: @@
 </file>
 Usage can be: \\
-iod: data and pedigree stored in disk. \\
+iod: data and pedigree stored in disk, using less memory. The iteration time depends on the HDD/SSD I/O access speed. \\
-iom: data and pedigree stored in memory. It uses less operations than iod.\\
+iom: data and pedigree stored in memory. It uses less operations than iod but more memory.\\
 map: data in disk and pedigree in memory. It uses less operations than iom. \\
 <file>
@@ Line 115: / Line 124: @@
 //For information on availability of BLUP90IOD3, please contact Ignacy Misztal (ignacy@uga.edu) at the University of Georgia.//
+===== Tips for running BLUP90IOD3 =====
+When the convergence is very slow or never reached, there are several reasons. One of the major issues is the left-hand-side in MME is close to non-positive definite.
+. The covariance matrix G and/or R is close to non-positive definite.\\
+In this case, change the tolerance value (xx) in the option:
+OPTION tol xx
+to a lenient value (e.g., 1d-04),
+which is similar to re-parameterization for G = VDV' using larger eigenvalue(s) in D.
+. Use "OPTION blksize xx cor" for a model with correlated random effects, where xx is the maximum size of (co)variance matrix for correlated random effects.
+. Remove the old data, which the contribution to the current active population is minimal.
+. Remove non-contribution animals, which have no relationships with other animals that have phenotypes.
+. Re-estimate the variance-covariance matrices accurately using the current data.
+. Remove animals with no phenotypes in the input data file. If those animals have relationships in the pedigree and/or the genotypes, they will be included in the renaddXX.ped (output pedigree file) after running renumf90. So, they do not need to be included in the phenotypic data file when they have no phenotypes.
+:\\
+: