Question: Why Plink stoped analyzing without make a new PED file and MAP file?
0
gravatar for Bahar
3.8 years ago by
Bahar40
Iran
Bahar40 wrote:

Hello every Friends

I ran following command in plink but my plink suddenly crashed and stop the analysis, although, I ran this command for several times without any problem!

plink --file oe24_2 --maf 0.01 --out oe24_3 --noweb

and it is my log file!

686698 (of 686698) markers to be included from [ oe24_2.map ]
11497 individuals read from [ oe24_2.ped ] 
0 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 11497 missing
5201 males, 6296 females, and 0 of unspecified sex
Before frequency and genotyping pruning, there are 686698 SNPs
5482 founders and 6015 non-founders found
1974783 heterozygous haploid genotypes; set to missing
Writing list of heterozygous haploid genotypes to [ oe24_3.hh ]
Total genotyping rate in remaining individuals is 0.985569
0 SNPs failed missingness test ( GENO > 1 )
61466 SNPs failed frequency test ( MAF < 0.01 )
After frequency and genotyping pruning, there are 625232 SNPs
After filtering, 0 cases, 0 controls and 11497 missing
After filtering, 5201 males, 6296 females, and 0 of unspecified sex

Analysis finished: Tue Nov  3 19:47:49 2015

any body can help me why plink doesn't make a new PED and MAP file?

 

gwas snp genome software error • 1.0k views
ADD COMMENTlink modified 3.8 years ago by chrchang5235.5k • written 3.8 years ago by Bahar40
1
gravatar for chrchang523
3.8 years ago by
chrchang5235.5k
United States
chrchang5235.5k wrote:

You forgot to include --recode in your command line.

ADD COMMENTlink written 3.8 years ago by chrchang5235.5k

OOOOOH!
YES!
thanks so much! 

I miss 2 days for stupid mistake! :(

ADD REPLYlink written 3.8 years ago by Bahar40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 782 users visited in the last hour