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/test-data/rgGLMtest1_GLM_log.txt

https://bitbucket.org/cistrome/cistrome-harvard/
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 1rgGLM.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']
 2vcl=['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']
 3xformQassoc got resf=/tmp/tmpXKEn_LrgGLM/tinywga.assoc.linear, outfname=/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls
 4###maxp=1.188425,minp=0.046772,prange=1.641653,scalefact=609.142127
 5
 6
 7@----------------------------------------------------------@
 8|        PLINK!       |     v1.07      |   10/Aug/2009     |
 9|----------------------------------------------------------|
10|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
11|----------------------------------------------------------|
12|  For documentation, citation & bug-report instructions:  |
13|        http://pngu.mgh.harvard.edu/purcell/plink/        |
14@----------------------------------------------------------@
15
16Skipping web check... [ --noweb ] 
17Writing this text to log file [ tinywga.log ]
18Analysis started: Sun May  9 21:23:49 2010
19
20Options in effect:
21	--noweb
22	--bfile /share/shared/galaxy/test-data/tinywga
23	--pheno-name c1
24	--pheno /share/shared/galaxy/test-data/tinywga.pphe
25	--out tinywga
26	--mind 1
27	--geno 1
28	--maf 0
29	--linear
30
31Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
3225 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
33Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
3440 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
3540 individuals with nonmissing phenotypes
36Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
37Missing phenotype value is also -9
3810 cases, 30 controls and 0 missing
3921 males, 19 females, and 0 of unspecified sex
40Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
41Detected that binary PED file is v1.00 SNP-major mode
42Reading alternate phenotype from [ /share/shared/galaxy/test-data/tinywga.pphe ] 
4340 individuals with non-missing alternate phenotype
44Assuming a quantitative trait
45Missing phenotype value is -9
46Before frequency and genotyping pruning, there are 25 SNPs
4727 founders and 13 non-founders found
48Total genotyping rate in remaining individuals is 0.995
490 SNPs failed missingness test ( GENO > 1 )
500 SNPs failed frequency test ( MAF < 0 )
51After frequency and genotyping pruning, there are 25 SNPs
52After filtering, 40 individuals with non-missing status
53After filtering, 21 males, 19 females, and 0 of unspecified sex
54Converting data to Individual-major format
55Writing linear model association results to [ tinywga.assoc.linear ] 
56
57Analysis finished: Sun May  9 21:23:49 2010
58