ERROR: Stopping as there are no SNPs left for analysis

Question

[r.asadpur]

Hello dear all

I've problem with using plink when I use this command in plink I received this massage

The command is

plink --bfile gwas --cow --linear --adjust --out assoc

and error is

@----------------------------------------------------------@
|        PLINK!       |     v1.02      |   25/May/2008     |
|----------------------------------------------------------|
|  (C) 2008 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Web-check not implemented on this system...
Writing this text to log file [ assoc1.log ]
Analysis started: Fri Jul 31 06:03:20 2015

Options in effect:
    --bfile gwas
    --sheep
    --linear
    --adjust
    --out assoc1

Reading map (extended format) from [ gwas.bim ] 
213 markers to be included from [ gwas.bim ]
Reading pedigree information from [ gwas.fam ] 
500 individuals read from [ gwas.fam ] 
500 individuals with nonmissing phenotypes
Assuming a quantitative trait
Missing phenotype value is -9
248 males, 252 females, and 0 of unspecified sex
Reading genotype bitfile from [ gwas.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 213 SNPs
0 founders and 500 non-founders found
0 of 500 individuals removed for low genotyping ( MIND > 0.1 )
213 SNPs with no founder genotypes observed
Warning, MAF set to 0 for these SNPs (see --nonfounders)
Writing list of these SNPs to [ assoc1.nof ]
Total genotyping rate in remaining individuals is 1
0 SNPs failed missingness test ( GENO > 0.1 )
213 SNPs failed frequency test ( MAF < 0.01 )
After frequency and genotyping pruning, there are 0 SNPs

ERROR: Stopping as there are no SNPs left for analysis

Thanks
asadpur!

Answer 1

[karl.stamm]

It's not a software error. Read the output.

Before frequency and genotyping pruning, there are 213 SNPs

213 SNPs failed frequency test ( MAF < 0.01 )

That's it, all markers were omitted. Change that setting if you want to use rare SNPs or if you didn't intend these to be rare SNPs, there's a problem with the data.