plink.log

@----------------------------------------------------------@
|        PLINK!       |     v1.07      |   10/Aug/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

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

Problem connecting to web

Writing this text to log file [ /mnt/httpd/bioinfo/opencga_0.4.0/jobs/J_qEcv8CA1Av//plink.log ]
Analysis started: Tue Jan 27 16:32:17 2015

Options in effect:
	--ped /mnt/httpd/bioinfo/opencga_0.4.0/jobs/J_qEcv8CA1Av/job.ped
	--map /mnt/httpd/bioinfo/opencga_0.4.0/jobs/J_qEcv8CA1Av/job.map
	--out /mnt/httpd/bioinfo/opencga_0.4.0/jobs/J_qEcv8CA1Av//plink
	--maf 0.02
	--assoc

** For gPLINK compatibility, do not use '.' in --out **
499264 (of 500568) markers to be included from [ /mnt/httpd/bioinfo/opencga_0.4.0/jobs/J_qEcv8CA1Av/job.map ]
162 individuals read from [ /mnt/httpd/bioinfo/opencga_0.4.0/jobs/J_qEcv8CA1Av/job.ped ] 
162 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
54 cases, 108 controls and 0 missing
98 males, 64 females, and 0 of unspecified sex
 *** WARNING *** DUPLICATE MARKERS FOUND *** 
Duplicate marker name found: [ rs41388745 ]

Before frequency and genotyping pruning, there are 499264 SNPs
108 founders and 54 non-founders found
9192 heterozygous haploid genotypes; set to missing
Writing list of heterozygous haploid genotypes to [ /mnt/httpd/bioinfo/opencga_0.4.0/jobs/J_qEcv8CA1Av//plink.hh ]
Total genotyping rate in remaining individuals is 0.958639
0 SNPs failed missingness test ( GENO > 1 )
81256 SNPs failed frequency test ( MAF < 0.02 )
After frequency and genotyping pruning, there are 418008 SNPs
After filtering, 54 cases, 108 controls and 0 missing
After filtering, 98 males, 64 females, and 0 of unspecified sex
Writing main association results to [ /mnt/httpd/bioinfo/opencga_0.4.0/jobs/J_qEcv8CA1Av//plink.assoc ] 

Analysis finished: Tue Jan 27 16:33:58 2015