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  Announcements  ~  Gblup does not provide solutions for some IDs in the pedigre

nasirshalizi
Posted: Tue Jun 09, 2020 8:28 pm Reply with quote
Joined: 19 Sep 2018 Posts: 1
Hello,

I am trying to fit a Gblup model in ASReml standalone. There are 2065 entries in the pedigree of which 2023 are genotypes and 42 are parents and grandparents. I have SNP marker data for 2023 genotypes and 20 parents. I do not have SNP data for 22 other parents and grandparents. I calculated the genomic relationship matrix for 2043 IDs and converted that into a GIV file. I fitted a simple additive genetic effect to check whether the model works fine. The model converges and things look fine in the asr file. But when I look at the SLN and PVS files, the model does not provide solutions and or predictions for 22 IDs. I checked the order of genotypes and matched it with the pedigree. The GIV file is missing 22 parents that were not genotyped but I sorted the genomic relationship matrix as it appears in the pedigree. I am not sure why the model is not providing the solutions for 22 genotypes. I know it has something to do with the 22 non-genotyped parents but I am not sure how to fix it to get solutions and predictions for all 2023 genotypes and 42 parents.
Below is the asr output. I also attached SLN and PVS files. Any help and suggestion would be appreciated.
Thanks,
Nasir



ASReml 4.2 [01 Jan 2016] Title: ACE Gblup analysis.
Build mv [18 Dec 2019] 64 bit Windows x64
09 Jun 2020 12:23:37.893 16026 Mbyte ktop\ACE1\asreml2\out/ACE9_VOL
Licensed to: North Carolina State University 30-nov-2020
*****************************************************************
* Contact support@asreml.co.uk for licensing and support *
*********************************************************** ARG *
Folder: C:\Users\nasir\Desktop\ACE1\asreml2
CLONE !P
FSCLONE !A
FAMILY !A
TYPE !A
ACE_ped.csv !SKIP 1 !ALPHA !SORT !GIV !DIAG
Notice: Sorted pedigree written to: ACE_ped.csv.SRT
First 42 rows are parents.
Reading pedigree file ACE_ped.csv.SRT: skipping 1 lines
Pedigree Header Line: ID,Female,Male
Pedigree check: Male N07056 previously occurred as a Fema Now at line 42: N111062 N11010 N07056
Pedigree check: Fema N11010 previously occurred as a Male Now at line 42: N111062 N11010 N07056
Pedigree check: Male N11210 previously occurred as a Fema Now at line 131: ACE_04X01 N21209 N11210
Pedigree check: Male N11249 previously occurred as a Fema Now at line 245: ACE_08X01 N11281 N11249
Pedigree check: Male N11266 previously occurred as a Fema Now at line 281: ACE_09X02 N11281 N11266
Pedigree check: Fema N111069 previously occurred as a Male Now at line 523: ACE_21X02 N111069 N071029
Pedigree check: Male N111066 previously occurred as a Fema Now at line 1116: ACE_48X01 N111111 N111066
Pedigree check: Male N111111 previously occurred as a Fema Now at line 1323: ACE_55X13 N111128 N111111
Pedigree check: Male N111128 previously occurred as a Fema Now at line 1448: ACE_63X02 N11220 N111128
Pedigree check: Male N11225 previously occurred as a Fema Now at line 1577: ACE_66X01 N11220 N11225
15 individuals appear as both male and female parent
2065 identities in the pedigree over 3+ generations.
For first parent labelled Fema, second labelled Male
Fema Fema_of_Fema Male_of_Fema Male Fema_of_Male Male_of_Male
32 7 6 25 6 6
Using an adapted version of Meuwissen & Luo GSE 1992 305-313:
PEDIGREE [ACE_ped.csv.SRT ] has 2065 identities, 6126 Non zero elements

Reading C:\Users\nasir\Desktop\ACE1\asreml2\G.giv skipping 0
header lines
Inverse G structure of 2043 rows having 2087946 non zero cells read from C:\Users\nasir\Desktop\ACE1\asreml2\G.giv
GIV0 NRM 2065 7 -1382.81
GIV1 C:\Users\nas 2043 7 -0.00
QUALIFIERS: !SKIP 1
QUALIFIERS: !MAXIT 100 !CONTINUE
QUALIFIER: !DOPART 9 is active
Reading C:\Users\nasir\Desktop\ACE1\asreml2\ACE_data.csv FREE FORMAT skipping 1 lines

Univariate analysis of VOL
Summary of 11516 records retained of 11519 read

Model term Size #miss #zero MinNon0 Mean MaxNon0 StndDevn
1 CLONE !P 2065 0 0 43 1040 2065
2 FSCLONE 1954 299 0 1 945.6995 1954
3 TEST 8 0 0 1 4.0854 8
4 ROW 146 0 0 1 27.0572 146
5 COL 84 0 0 1 29.6149 84
6 STRT 353 0 1.000 3.408 6.000 1.239
7 RUST 0 10869 1.000 0.5618E-01 1.000 0.2303
8 VOL Variate 0 0 5.947 50.93 183.5 27.07
9 FAMILY 58 0 0 1 26.6803 58
10 TYPE 2 0 0 1 1.0260 2
11 STDVOL 0 0 97.07 100.0 105.0 0.9997
12 mu 1
Warning: GRM matrix is too SMALL
13 giv1(CLONE) 2043
14 idh(TEST) 8
15 idh(TEST).ROW 1168 14 idh(TEST) : 8 4 ROW : 146
16 idh(TEST).COL 672 14 idh(TEST) : 8 5 COL : 84
idh(TEST) in idh(TEST).COL has size 8, parameters: 17 24
idh(TEST).COL [17:24] initialized.
idh(TEST) in idh(TEST).ROW has size 8, parameters: 25 32
idh(TEST).ROW [25:32] initialized.
Forming 3892 equations: 9 dense.
Initial updates will be shrunk by factor 0.316
Notice: ReStartValues taken from C:\Users\nasir\Desktop\ACE1\asreml2\out/ACE9_VOL.rsv

Notice: # is honoured as a special white-out character in data file
Notice: Use !SPECIALCHAR to treat # as normal character in data file
* This job may use 12 of the 12 processor cores. !MP *
Notice: LogL values are reported relative to a base of -30000.000
Notice: 1 singularities detected in design matrix.
1 LogL=-8505.14 S2= 1.0000 11508 df
2 LogL=-8505.14 S2= 1.0000 11508 df
3 LogL=-8505.14 S2= 1.0000 11508 df

- - - Results from analysis of VOL - - -
Akaike Information Criterion 77060.28 (assuming 25 parameters).
Bayesian Information Criterion 77244.05

Model_Term Sigma Sigma Sigma/SE % C
giv1(CLONE) GRM_V 2043 31.4027 31.4027 9.38 0 P
sat(TEST,1).id(units) 1899 effects
Residual_1 SCA_V 1899 145.562 145.562 28.08 0 P
sat(TEST,2).id(units) 1583 effects
Residual_2 SCA_V 1583 920.123 920.123 26.95 0 P
sat(TEST,3).id(units) 1743 effects
Residual_3 SCA_V 1743 603.684 603.684 28.20 0 P
sat(TEST,4).id(units) 985 effects
Residual_4 SCA_V 985 129.879 129.879 19.64 0 P
sat(TEST,5).id(units) 1732 effects
Residual_5 SCA_V 1732 266.113 266.113 27.52 0 P
sat(TEST,6).id(units) 1561 effects
Residual_6 SCA_V 1561 512.861 512.861 26.01 0 P
sat(TEST,7).id(units) 1316 effects
Residual_7 SCA_V 1316 86.5134 86.5134 22.08 0 P
sat(TEST,8).id(units) 697 effects
Residual_8 SCA_V 697 48.6964 48.6964 14.59 0 P
idh(TEST).COL 672 effects
TEST DIAG_V 1 11.6155 11.6155 3.84 0 P
TEST DIAG_V 2 4.24047 4.24047 0.57 0 P
TEST DIAG_V 3 1.46150 1.46150 0.34 0 P
TEST DIAG_V 4 6.72778 6.72778 2.29 0 P
TEST DIAG_V 5 1.20975 1.20975 0.64 0 P
TEST DIAG_V 6 84.5800 84.5800 2.65 0 P
TEST DIAG_V 7 1.07176 1.07176 0.96 0 P
TEST DIAG_V 8 0.797852 0.797852 0.66 0 P
idh(TEST).ROW 1168 effects
TEST DIAG_V 1 64.9776 64.9776 4.20 0 P
TEST DIAG_V 2 20.4466 20.4466 2.01 0 P
TEST DIAG_V 3 7.24004 7.24004 1.49 0 P
TEST DIAG_V 4 14.6032 14.6032 3.12 0 P
TEST DIAG_V 5 13.0553 13.0553 3.07 0 P
TEST DIAG_V 6 3.41688 3.41688 0.54 0 P
TEST DIAG_V 7 6.52739 6.52739 2.64 0 P
TEST DIAG_V 8 0.593520 0.593520 0.77 0 P

Wald F statistics
Source of Variation NumDF F-inc
12 mu 1 416.42
3 TEST 7 928.47

Solution Standard Error T-value T-prev
3 TEST
2 39.0418 1.74864 22.33
3 42.5612 1.56328 27.23 2.68
4 15.4518 1.58553 9.75 -25.00
5 12.1835 1.53027 7.96 -3.16
6 28.8744 2.68743 10.74 6.94
7 7.00266 1.50244 4.66 -9.16
8 -12.4166 1.41803 -8.76 -27.89
12 mu
1 28.4362 2.13185 13.34
16 idh(TEST).COL 672 effects fitted ( 191 are zero)
15 idh(TEST).ROW 1168 effects fitted ( 771 are zero)
13 giv1(CLONE) 2043 effects fitted
* This job used at least 2100 of the 16026 Mbyte of primary workspace. *
SLOPES FOR LOG(ABS(RES)) on LOG(PV) for Section 11
0.69
7 possible outliers: see .res file
SLOPES FOR LOG(ABS(RES)) on LOG(PV) for Section 13
0.59
1 possible outliers: see .res file
SLOPES FOR LOG(ABS(RES)) on LOG(PV) for Section 14
0.65
SLOPES FOR LOG(ABS(RES)) on LOG(PV) for Section 15
0.49
2 possible outliers: see .res file
1 possible outliers: see .res file
SLOPES FOR LOG(ABS(RES)) on LOG(PV) for Section 18
0.52
Finished: 09 Jun 2020 12:24:42.381 LogL Converged



ACE12_VOL.sln
 Description:
Predictions file

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 Filename:  ACE12_VOL.sln
 Filesize:  279.09 KB
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ACE12_VOL.pvs
 Description:

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 Filename:  ACE12_VOL.pvs
 Filesize:  111.75 KB
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