Post by mehraj on Mar 2, 2016 1:47:31 GMT
Hi Jiang,
I tried to run LD stratifying option on the test file but it is returning with message as invalid option for the ld-score . Please help in matter.
Error: invalid option "--ld-score-region".
Analysis finished: Tue Mar 1 19:37:18 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile /programs/GCTA/test --ld-score-region --out /workdir/mus5/test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:37:41 2016
Options:
--bfile /programs/GCTA/test
Error: invalid option "--ld-score-region".
Analysis finished: Tue Mar 1 19:37:41 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile /programs/GCTA/test --ld-score-region --out /workdir/mus5/test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:37:46 2016
Options:
--bfile /programs/GCTA/test
Error: invalid option "--ld-score-region".
Analysis finished: Tue Mar 1 19:37:46 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ clear
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile /programs/GCTA/test --ld-score-region --out /workdir/mus5/test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:39:24 2016
Options:
--bfile /programs/GCTA/test
Error: invalid option "--ld-score-region".
Analysis finished: Tue Mar 1 19:39:24 2016
Computational time: 0:0:0
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:40:13 2016
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:42:29 2016
Options:
Error: no analysis has been launched by the option(s).
Analysis finished: Tue Mar 1 19:42:29 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile test --ldscore-region 200 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:43:33 2016
Options:
--bfile test
Error: invalid option "--ldscore-region".
Analysis finished: Tue Mar 1 19:43:33 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile test --ld-score-region 200 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile test --ld-score --ld-wind 1000 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:51:20 2016
Options:
--bfile test
Error: invalid option "--ld-score".
Analysis finished: Tue Mar 1 19:51:20 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile /programs/GCTA/test --ld-score --ld-wind 1000 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:53:03 2016
Options:
--bfile /programs/GCTA/test
Error: invalid option "--ld-score".
Analysis finished: Tue Mar 1 19:53:03 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile /programs/GCTA/test --ld-score --ld-wind 1000 --ld-rsq-cutoff 0.01 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 20:18:55 2016
Options:
--bfile /programs/GCTA/test
Error: invalid option "--ld-score".
Analysis finished: Tue Mar 1 20:18:55 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile /programs/GCTA/test --ld-score-region --ld-wind 1000 --ld-rsq-cutoff 0.01 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 20:19:22 2016
Options:
--bfile /programs/GCTA/test
Error: invalid option "--ld-score-region".
Analysis finished: Tue Mar 1 20:19:22 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$
I tried to run LD stratifying option on the test file but it is returning with message as invalid option for the ld-score . Please help in matter.
Error: invalid option "--ld-score-region".
Analysis finished: Tue Mar 1 19:37:18 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile /programs/GCTA/test --ld-score-region --out /workdir/mus5/test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:37:41 2016
Options:
--bfile /programs/GCTA/test
Error: invalid option "--ld-score-region".
Analysis finished: Tue Mar 1 19:37:41 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile /programs/GCTA/test --ld-score-region --out /workdir/mus5/test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:37:46 2016
Options:
--bfile /programs/GCTA/test
Error: invalid option "--ld-score-region".
Analysis finished: Tue Mar 1 19:37:46 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ clear
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile /programs/GCTA/test --ld-score-region --out /workdir/mus5/test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:39:24 2016
Options:
--bfile /programs/GCTA/test
Error: invalid option "--ld-score-region".
Analysis finished: Tue Mar 1 19:39:24 2016
Computational time: 0:0:0
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:40:13 2016
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:42:29 2016
Options:
Error: no analysis has been launched by the option(s).
Analysis finished: Tue Mar 1 19:42:29 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile test --ldscore-region 200 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:43:33 2016
Options:
--bfile test
Error: invalid option "--ldscore-region".
Analysis finished: Tue Mar 1 19:43:33 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile test --ld-score-region 200 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile test --ld-score --ld-wind 1000 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:51:20 2016
Options:
--bfile test
Error: invalid option "--ld-score".
Analysis finished: Tue Mar 1 19:51:20 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile /programs/GCTA/test --ld-score --ld-wind 1000 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 19:53:03 2016
Options:
--bfile /programs/GCTA/test
Error: invalid option "--ld-score".
Analysis finished: Tue Mar 1 19:53:03 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile /programs/GCTA/test --ld-score --ld-wind 1000 --ld-rsq-cutoff 0.01 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 20:18:55 2016
Options:
--bfile /programs/GCTA/test
Error: invalid option "--ld-score".
Analysis finished: Tue Mar 1 20:18:55 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$ /programs/GCTA/gcta64 --bfile /programs/GCTA/test --ld-score-region --ld-wind 1000 --ld-rsq-cutoff 0.01 --out test
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Mar 1 20:19:22 2016
Options:
--bfile /programs/GCTA/test
Error: invalid option "--ld-score-region".
Analysis finished: Tue Mar 1 20:19:22 2016
Computational time: 0:0:0
[mus5@cbsum1c2b004 mus5]$
