rgClean.py started, called as /share/shared/galaxy/tools/rgenetics/rgClean.py /share/shared/galaxy/test-data tinywga rgCleantest1 1 1 0 0 1 1 /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.pbed /share/shared/galaxy/test-data/rgtestouts/rgClean 0 0 0 0

@----------------------------------------------------------@
|        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/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ]
Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ]
Analysis started: Sun May  9 21:23:43 2010

Options in effect:
--noweb
--bfile /share/shared/galaxy/test-data/tinywga
--make-bed
--out /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1
--set-hh-missing
--mind 1
--geno 1
--maf 0
--hwe 0
--me 1 1

Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ]
25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ]
40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ]
40 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
10 cases, 30 controls and 0 missing
21 males, 19 females, and 0 of unspecified sex
Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ]
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 25 SNPs
27 founders and 13 non-founders found
0 markers to be excluded based on HWE test ( p <= 0 )
0 markers failed HWE test in cases
0 markers failed HWE test in controls
Total genotyping rate in remaining individuals is 0.995
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 25 SNPs
After filtering, 10 cases, 30 controls and 0 missing
After filtering, 21 males, 19 females, and 0 of unspecified sex
14 nuclear families, 1 founder singletons found
13 non-founders with 2 parents in 13 nuclear families
0 non-founders without 2 parents in 0 nuclear families
10 affected offspring trios
0 phenotypically discordant parent pairs found
Converting data to Individual-major format
Filtering SNPs/families for Mendel Error rates above 1, 1
0 Mendel errors detected in total
0 families ( 0 individuals ) removed due to Mendel errors
0 markers removed due to Mendel errors, 25 remaining
Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ]
Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ]
Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ]
Using (default) SNP-major mode
Converting data to SNP-major format

Analysis finished: Sun May  9 21:23:43 2010