I tried LD based puring by plink v 1.07, and waited long time. however, the prune.in and prune.out are blank.

I do not know if it is finished.

The log is as following:

@----------------------------------------------------------@
|         PLINK!       |    v0.99o     |   20/Nov/2006     |
|----------------------------------------------------------|
|  (C) 2006 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|       http://pngu.mgh.harvard.edu/purcell/plink/         |
@----------------------------------------------------------@

Web-based version check ( --noweb to skip )
Connecting to web...  failed connection

Writing this text to log file [ A1_pruning.log ]
Analysis started: Fri Apr 24 10:55:44 2015

Options in effect:
 --file A1.plk
 --nonfounders
 --allow-no-sex
 --indep-pairwise 50 5 0.5
 --out A1_pruning
 --silent

774 (of 774) markers to be included from [ A1.plk.map ]
174 individuals read from [ A1.plk.ped ]
0 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases and 0 controls
Before frequency and genotyping pruning, there are 774 SNPs
Applying filters (SNP-major mode)
0 founders and 174 non-founders found
Writing list of removed individuals to [ A1_pruning.irem ]
4 of 174 individuals removed for low genotyping ( MIND > 0.1 )
Total genotyping rate in remaining individuals is 0.987103
27 SNPs failed missingness test ( GENO > 0.1 )
0 SNPs failed frequency test ( MAF < 0.01 )
After frequency and genotyping pruning, there are 747 SNPs
Performing LD-based pruning...
Writing pruned-in SNPs to [ A1_pruning.prune.in ]
Writing pruned-out SNPs to [ A1_pruning.prune.out ]