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BLUPF90 public forum (beta test)

This website is a public area for open discussion about a public version of BLUPF90 and related programs.

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The support is community-based. Any people, regardless of whether they belong to the University of Georgia or not, may provide an answer to a question, useful information, and a pointer to a useful website. It is not guaranteed that you timely receive a correct answer or a useful comment.

For now, there are two options where you post your question, suggestion, or bug report.

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  • Operating system (Windows, Linux, Mac OS, etc.)
  • What you did, and what you get on screen or in files
  • Parameter file in use and the output message on screen
  • Small examples to reproduce the issue (if possible)

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blupf90-public's Issues

2019 update error "ID from SNP file not found"

I am running BLUPf90 on linux and recently updated it. Prior to the update the code and data bellow produced a Manhattan plot showing SNP effect, but after the update using the same files when I run renumf90 for the first parameter file I get an error "ID from SNP file not found." Also the number of animals with records and the number of animals with genotypes are the same but the number with records or genotypes and total number are doubled and the number with genotypes and no records is the same as with records and with genotypes. So I think its reading the IDs in the SNP file as different from the IDs in the pedigree but I'm not sure why it would do that. Should I be formatting any of my files differently now because of the update?

image

data.txt:
1409 44.4706 47.6518 7.8578
1441 46.3259 45.5345 8.1068
1450 47.1158 46.6434 6.2249
0828 50.722 43.6634 5.5959
0834 49.1265 44.1306 6.714
image

pedigree.txt
1409 0 0
1441 0 0
1450 0 0
0828 0 0
0834 0 0
image

genotypes.txt
1409 0521550
1441 2021101
1450 1255112
0828 5122011
0834 0110225
image

SSGBLUP1.txt:
DATAFILE
data.txt
TRAITS
2
FIELDS_PASSED TO OUTPUT

WEIGHT(S)

RESIDUAL_VARIANCE
2.5
EFFECT
1 cross num
RANDOM
animal
FILE
pedigree.txt
FILE_POS
1 2 3 0 0
SNP_FILE
genotypes.txt
(CO)VARIANCES
0.07
OPTION saveGInverse
OPTION saveA22Inverse
OPTION chrinfo map
OPTION minfreq 0.05
OPTION callrate 0.90
OPTION callrateAnim 0.85
OPTION solution mean 1 2 3
OPTION sol se
SSGBLUP1.txt

SSGBLUP2.txt:
DATAFILE
data.txt
TRAITS
2
FIELDS_PASSED TO OUTPUT

WEIGHT(S)

RESIDUAL_VARIANCE
2.5
EFFECT
1 cross num
RANDOM
animal
FILE
pedigree.txt
FILE_POS
1 2 3 0 0
SNP_FILE
genotypes.txt
(CO)VARIANCES
0.07
OPTION readGInverse
OPTION readA22Inverse
OPTION chrinfo map
OPTION minfreq 0.05
OPTION callrate 0.90
OPTION callrateAnim 0.85
OPTION windows_variance 20
OPTION which_weight 1
OPTION snp_effect_gebv
SSGBLUP2.txt

module load blupf90
renumf90
SSGBLUP1.txt
blupf90
renf90.par
renumf90
SSGBLUP2.txt
postGSf90
renf90.par

The SSblup problem

Dear group,
The new tutorial blupf90 (2019) maybe has a problem, in “8.5 GWAS using the ssGBLUP framework”, I download the data from http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=lab_gwas.zip - lab_gaws.zip, then run it. But when I do the “bash s1.sh”, the computer give me the information:

cp: impossible d'évaluer 'snp_sol': Aucun fichier ou dossier de ce type
cp: impossible d'évaluer 'chrsnp': Aucun fichier ou dossier de ce type
awk: cannot open snp_sol (No such file or directory)

image

.
So I try did it used one by one parameter file, but when I run the blupf90(renf90.par), there also had this problem.
Can you check the data?

Kind regard,
Yansen

gibbs3f90 : When permanent environment is fixed to zero, residual (co)variances become huge

Dear all,

I want to run a multivariate animal model with 3 traits. Only one of them have repeated measurements.
I fixed the PE-environment variances and covariances to zero for the two traits without repeated measurment.

Problem: Genetic and residual variances and covariances continue to increase with iterations until they reach numbers in the order of 10e+7 digits. This behavior occurs for all traits.

This problem can be reproduced by simply fitting any multivariate animal model with a "pe part" set to zero.
There's probably something I'm missing.

Is there a proper way to fit a multivariate animal model with both repeated/no-repeated traits?

Best

S

how to use BLUPF90

With data0.txt and param0.txt in the Tutorial BLUPF90 I can't run BLUPF90 in windows 32-bit. Nothing on the computer screen I have installed Fortran compiler and file libiomp5md.dll as suggeested. Please help me. Thanks

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