Hi all,
Can anyone offer any advise as to why the prune.in and prune.out files from plink are both empty (info below)?
Many thanks if you can help at all
#./plink --noweb --allow-no-sex --batch_1.plink.ped –-indep 50 5 2
Skipping web check... [ --noweb ]
Writing this text to log file [ plink.log ]
Options in effect:
--noweb
--allow-no-sex
--file batch_1.plink
--indep 50 5 2
2665 (of 2665) markers to be included from [ batch_1.plink.map ]
Warning, found 24 individuals with ambiguous sex codes
Writing list of these individuals to [ plink.nosex ]
24 individuals read from [ batch_1.plink.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 24 missing
0 males, 0 females, and 24 of unspecified sex
Before frequency and genotyping pruning, there are 2665 SNPs
24 founders and 0 non-founders found
Total genotyping rate in remaining individuals is 0.950813
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 2665 SNPs
After filtering, 0 cases, 0 controls and 24 missing
After filtering, 0 males, 0 females, and 24 of unspecified sex
Performing LD-based pruning...
Writing pruned-in SNPs to [ plink.prune.in ]
Writing pruned-out SNPs to [ plink.prune.out ]
Scanning from chromosome 0 to 0
Skippng chromosome 0
