Question: Plink prune.in prune.out blank
0
gravatar for jt358
4.4 years ago by
jt35810
jt35810 wrote:

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

snp • 2.5k views
ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 4.4 years ago by jt35810
0
gravatar for chrchang523
4.4 years ago by
chrchang5236.9k
United States
chrchang5236.9k wrote:

Variants with a chromosome code of 0 are considered to be unplaced, and are ignored by --indep{-pairwise}.

ADD COMMENTlink written 4.4 years ago by chrchang5236.9k
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