Post by jgoudet on Jul 16, 2019 22:29:11 GMT
Hi all, I am trying to run an asociation test, and have been successful previously, but I encounter the following with one of my simulated data set:
Analysis started at 16:30:46 UTC on Tue Jul 16 2019.
Accepted options:
--mlma
--bfile adm8
--grm adm8gcta
--pheno pheno_nm.txt
--mpheno 50
--out adm8_nm_asstest_gcta50
--thread-num 20
Note: the program will be running on 20 threads.
Reading PLINK FAM file from [adm8.fam].
3000 individuals to be included from [adm8.fam].
Reading PLINK BIM file from [adm8.bim].
994596 SNPs to be included from [adm8.bim].
Warning: Duplicated SNP ID "M_994595" has been changed to "M_994595_994596"
.Reading PLINK BED file from [adm8.bed] in SNP-major format ...
Genotype data for 3000 individuals and 994596 SNPs to be included from [adm8.bed].
Accepted options:
--mlma
--bfile adm8
--grm adm8gcta
--pheno pheno_nm.txt
--mpheno 50
--out adm8_nm_asstest_gcta50
--thread-num 20
Note: the program will be running on 20 threads.
Reading PLINK FAM file from [adm8.fam].
3000 individuals to be included from [adm8.fam].
Reading PLINK BIM file from [adm8.bim].
994596 SNPs to be included from [adm8.bim].
Warning: Duplicated SNP ID "M_994595" has been changed to "M_994595_994596"
.Reading PLINK BED file from [adm8.bed] in SNP-major format ...
Genotype data for 3000 individuals and 994596 SNPs to be included from [adm8.bed].
The analysis run, but only for 994596 SNPs instead of the 1727769 intended.
The BED file used does not seem to have any issue, I don't see any duplicate SNPs, and plink reports the correct number of SNPs with the same BED file:
wc -l plink.snplist
1727769 plink.snplist
1727769 plink.snplist
Any idea what could be wrong? Many thanks in advance