Why Plink stoped analyzing without make a new PED file and MAP file?

Question

[Bahar]

Hello 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 this 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

Can anybody help me why plink doesn't make a new PED and MAP file?

Answer 1

[chrchang523]

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

[Bahar]

OOOOOH!
YES!
thanks so much!

I miss 2 days for stupid mistake! :(

[Dhara Awasthi]

Hi, I had a similar issue. The command prompt shows that output files are written but I can't see them. I don't know where the output and log files are getting saved.

I used this:

./plink --bfile HapMap_3_r3_1 --geno 0.2 --make-bed --recode --out HapMap_3_r3_2 --noweb

Please help me!