Post by yrldj on Jan 30, 2018 22:46:29 GMT
Hi,
I would really appreciate the help to understand why is my code not working. The error is "Abort trap 6". I just follow the instruction under "GREML in family data" section using the test data set coming with the GCTA 1.91.1.
gcta64 --bfile test --make-grm --out test
gcta64 --grm test --make-bK 0.05 --out test_bK
gcta64 --reml --mgrm mgrm.txt --pheno test.phen --out test_bKsK
The output:
*******************************************************************
Analysis started: Tue Jan 30 17:37:17 2018 EST
Hostname: LibodeMacBook-Air.local
Accepted Options:
--reml
--mgrm mgrm.txt
--pheno test.phen
--out test.bksk
Note: This is a multi-thread program. You could specify the number of threads by the --thread-num option to speed up the computation if there are multiple processors in your machine.
Reading phenotypes from [test.phen].
Non-missing phenotypes of 3925 individuals are included from [test.phen].
There are 2 GRM file names specified in the file [mgrm.txt].
Reading the GRM from the 1th file ...
Reading IDs of the GRM from [test.grm.id].
3925 IDs read from [test.grm.id].
Reading the GRM from [test.grm.bin].
GRM for 3925 individuals are included from [test.grm.bin].
Reading the GRM from the 2th file ...
Reading IDs of the GRM from [test_bK.grm.id].
3925 IDs read from [test_bK.grm.id].
Reading the GRM from [test_bK.grm.bin].
GRM for 3925 individuals are included from [test_bK.grm.bin].
3925 individuals are in common in these files.
Performing REML analysis ... (Note: may take hours depending on sample size).
3925 observations, 1 fixed effect(s), and 3 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 13.3339 6.8617 0.851676
logL: -2152.89
Running AI-REML algorithm ...
Iter. logL V(G1) V(G2) V(e)
1 -48724.58 13.33390 6.86172 0.85324
2 -48727.58 13.33380 6.86178 0.85818
....
97 -49629.89 13.32372 6.86834 1.32790
98 -49639.39 13.32362 6.86841 1.33285
99 -49648.89 13.32351 6.86848 1.33779
Abort trap: 6
*************************************************
When I apply the same kind of code on my own data (family-based genotype data), the same error occurred. I have changed computer, system (Windows/Mac), but doesn't work.
Thanks in advance,
Jing
I would really appreciate the help to understand why is my code not working. The error is "Abort trap 6". I just follow the instruction under "GREML in family data" section using the test data set coming with the GCTA 1.91.1.
gcta64 --bfile test --make-grm --out test
gcta64 --grm test --make-bK 0.05 --out test_bK
gcta64 --reml --mgrm mgrm.txt --pheno test.phen --out test_bKsK
The output:
*******************************************************************
Analysis started: Tue Jan 30 17:37:17 2018 EST
Hostname: LibodeMacBook-Air.local
Accepted Options:
--reml
--mgrm mgrm.txt
--pheno test.phen
--out test.bksk
Note: This is a multi-thread program. You could specify the number of threads by the --thread-num option to speed up the computation if there are multiple processors in your machine.
Reading phenotypes from [test.phen].
Non-missing phenotypes of 3925 individuals are included from [test.phen].
There are 2 GRM file names specified in the file [mgrm.txt].
Reading the GRM from the 1th file ...
Reading IDs of the GRM from [test.grm.id].
3925 IDs read from [test.grm.id].
Reading the GRM from [test.grm.bin].
GRM for 3925 individuals are included from [test.grm.bin].
Reading the GRM from the 2th file ...
Reading IDs of the GRM from [test_bK.grm.id].
3925 IDs read from [test_bK.grm.id].
Reading the GRM from [test_bK.grm.bin].
GRM for 3925 individuals are included from [test_bK.grm.bin].
3925 individuals are in common in these files.
Performing REML analysis ... (Note: may take hours depending on sample size).
3925 observations, 1 fixed effect(s), and 3 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 13.3339 6.8617 0.851676
logL: -2152.89
Running AI-REML algorithm ...
Iter. logL V(G1) V(G2) V(e)
1 -48724.58 13.33390 6.86172 0.85324
2 -48727.58 13.33380 6.86178 0.85818
....
97 -49629.89 13.32372 6.86834 1.32790
98 -49639.39 13.32362 6.86841 1.33285
99 -49648.89 13.32351 6.86848 1.33779
Abort trap: 6
*************************************************
When I apply the same kind of code on my own data (family-based genotype data), the same error occurred. I have changed computer, system (Windows/Mac), but doesn't work.
Thanks in advance,
Jing