Post by sk427 on Dec 13, 2019 5:31:02 GMT
Thank you for your great contribution.
I tried to use GCTA 1.93.0, and got an error like following.
In addition, --make-grm-part is also not working.
I found this error message ("Empty sample_subset is not currently permitted") in the source code of plink2 api (https://github.com/chrchang/plink-ng/blob/master/2.0/Python/pgenlib.pyx), also.
Any comments and suggestions are appriciated!
sk
*******************************************************************
* 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 05:23:22 UTC on Fri Dec 13 2019.
Hostname: tiger01
Options:
--make-grm
--chr 22
--bfile ../tmp/OE13.tag.sample
--thread-num 10
--out ../tmp/OE13.1.tag
The program will be running on up to 10 threads.
Note: GRM is computed using the SNPs on the autosome.
Reading PLINK FAM file from [../tmp/OE13.tag.sample.fam]...
1885 individuals to be included from FAM file.
1885 individuals to be included. 0 males, 0 females, 1885 unknown.
Reading PLINK BIM file from [../tmp/OE13.tag.sample.bim]...
962 SNPs to be included from BIM file(s).
24 SNPs to be included from valid chromosome number
Computing the genetic relationship matrix (GRM) v2 ...
Subset 1/1, no. subject 1-1885
1885 samples, 24 markers, 1777555 GRM elements
IDs for the GRM file has been saved in the file [../tmp/OE13.1.tag.grm.id]
Empty sample_subset is not currently permitted
I tried to use GCTA 1.93.0, and got an error like following.
In addition, --make-grm-part is also not working.
I found this error message ("Empty sample_subset is not currently permitted") in the source code of plink2 api (https://github.com/chrchang/plink-ng/blob/master/2.0/Python/pgenlib.pyx), also.
Any comments and suggestions are appriciated!
sk
*******************************************************************
* 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 05:23:22 UTC on Fri Dec 13 2019.
Hostname: tiger01
Options:
--make-grm
--chr 22
--bfile ../tmp/OE13.tag.sample
--thread-num 10
--out ../tmp/OE13.1.tag
The program will be running on up to 10 threads.
Note: GRM is computed using the SNPs on the autosome.
Reading PLINK FAM file from [../tmp/OE13.tag.sample.fam]...
1885 individuals to be included from FAM file.
1885 individuals to be included. 0 males, 0 females, 1885 unknown.
Reading PLINK BIM file from [../tmp/OE13.tag.sample.bim]...
962 SNPs to be included from BIM file(s).
24 SNPs to be included from valid chromosome number
Computing the genetic relationship matrix (GRM) v2 ...
Subset 1/1, no. subject 1-1885
1885 samples, 24 markers, 1777555 GRM elements
IDs for the GRM file has been saved in the file [../tmp/OE13.1.tag.grm.id]
Empty sample_subset is not currently permitted