Post by anamaria on Sept 2, 2020 18:14:30 GMT
Hello,
I downloaded GCTA for Linux from cnsgenomics.com/software/gcta/index.html#Download
I unzipped the directory and in gcta/gcta_1.93.0beta $ I did:
./gcta64 --reml-bivar --reml-bivar-nocove --grm test --pheno test.phen --reml-bivar-lrt-rg 0 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.93.0 beta Linux
* (C) 2010-2019, The University of Queensland
* Please report bugs to Jian Yang <jian.yang@uq.edu.au>
*******************************************************************
Analysis started at 18:10:43 UTC on Wed Sep 02 2020.
Hostname: login-1.saber.acer.uic.edu
Accepted options:
--reml-bivar 1 2
--reml-bivar-nocove
--grm test
--pheno test.phen
--reml-bivar-lrt-rg 0
--out test
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 IDs of the GRM from [test.grm.id].
Error: can not open the file [test.grm.id] to read.
An error occurs, please check the options or data
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.93.0 beta Linux
* (C) 2010-2019, The University of Queensland
* Please report bugs to Jian Yang <jian.yang@uq.edu.au>
*******************************************************************
Analysis started at 18:10:43 UTC on Wed Sep 02 2020.
Hostname: login-1.saber.acer.uic.edu
Accepted options:
--reml-bivar 1 2
--reml-bivar-nocove
--grm test
--pheno test.phen
--reml-bivar-lrt-rg 0
--out test
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 IDs of the GRM from [test.grm.id].
Error: can not open the file [test.grm.id] to read.
An error occurs, please check the options or data
Please advise how to run this test example.
I tried to run:
./gcta64 --bfile test --make-grm-bin --out test
and:
./gcta64 --reml-bivar --reml-bivar-nocove --grm test --pheno test.phen --reml-bivar-lrt-rg 0 --out test
but I got:
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 phenotypes from [test.phen].
Error: can not find the 2th trait in the file [test.phen].
An error occurs, please check the options or data
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 phenotypes from [test.phen].
Error: can not find the 2th trait in the file [test.phen].
An error occurs, please check the options or data
I am planning to run this on case/control pheno file that looks like this:
0 fam0110_G110 2
0 fam0113_G113 2
0 fam0114_G114 2
0 fam0117_G117 2
0 fam0118_G118 NA
0 fam0119_G119 1
0 fam0113_G113 2
0 fam0114_G114 2
0 fam0117_G117 2
0 fam0118_G118 NA
0 fam0119_G119 1
...
Do I need to reformat this as well?
Thanks