rgGLM.py called with ['/share/shared/galaxy/tools/rgenetics/rgGLM.py', '/share/shared/galaxy/test-data/tinywga', '/share/shared/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls', '/share/shared/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/share/shared/galaxy/test-data/rgGLMtest1_GLM_topTable.gff']
vcl=['plink', '--noweb', '--bfile', '/share/shared/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/share/shared/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear']
xformQassoc got resf=/tmp/tmpXKEn_LrgGLM/tinywga.assoc.linear, outfname=/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls
###maxp=1.188425,minp=0.046772,prange=1.641653,scalefact=609.142127


@----------------------------------------------------------@
|        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 [ tinywga.log ]
Analysis started: Sun May  9 21:23:49 2010

Options in effect:
	--noweb
	--bfile /share/shared/galaxy/test-data/tinywga
	--pheno-name c1
	--pheno /share/shared/galaxy/test-data/tinywga.pphe
	--out tinywga
	--mind 1
	--geno 1
	--maf 0
	--linear

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
Reading alternate phenotype from [ /share/shared/galaxy/test-data/tinywga.pphe ] 
40 individuals with non-missing alternate phenotype
Assuming a quantitative trait
Missing phenotype value is -9
Before frequency and genotyping pruning, there are 25 SNPs
27 founders and 13 non-founders found
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, 40 individuals with non-missing status
After filtering, 21 males, 19 females, and 0 of unspecified sex
Converting data to Individual-major format
Writing linear model association results to [ tinywga.assoc.linear ] 

Analysis finished: Sun May  9 21:23:49 2010