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/test-data/rgtestouts/rgQC/ldp_tinywga.log

https://bitbucket.org/cistrome/cistrome-harvard/
Unknown | 48 lines | 42 code | 6 blank | 0 comment | 0 complexity | 72d486b579ef4126370c435ba1e8c4a8 MD5 | raw file
 1
 2@----------------------------------------------------------@
 3|        PLINK!       |     v1.06      |   24/Apr/2009     |
 4|----------------------------------------------------------|
 5|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
 6|----------------------------------------------------------|
 7|  For documentation, citation & bug-report instructions:  |
 8|        http://pngu.mgh.harvard.edu/purcell/plink/        |
 9@----------------------------------------------------------@
10
11Skipping web check... [ --noweb ] 
12Writing this text to log file [ ldp_tinywga.log ]
13Analysis started: Wed May 19 15:15:38 2010
14
15Options in effect:
16	--noweb
17	--bfile /opt/galaxy/test-data/tinywga
18	--extract tinywga.prune.in
19	--make-bed
20	--out ldp_tinywga
21
22Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
2325 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
24Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
2540 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
2640 individuals with nonmissing phenotypes
27Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
28Missing phenotype value is also -9
2910 cases, 30 controls and 0 missing
3021 males, 19 females, and 0 of unspecified sex
31Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
32Detected that binary PED file is v1.00 SNP-major mode
33Reading list of SNPs to extract [ tinywga.prune.in ] ... 14 read
34Before frequency and genotyping pruning, there are 14 SNPs
3527 founders and 13 non-founders found
36Total genotyping rate in remaining individuals is 0.991071
370 SNPs failed missingness test ( GENO > 1 )
380 SNPs failed frequency test ( MAF < 0 )
39After frequency and genotyping pruning, there are 14 SNPs
40After filtering, 10 cases, 30 controls and 0 missing
41After filtering, 21 males, 19 females, and 0 of unspecified sex
42Writing pedigree information to [ ldp_tinywga.fam ] 
43Writing map (extended format) information to [ ldp_tinywga.bim ] 
44Writing genotype bitfile to [ ldp_tinywga.bed ] 
45Using (default) SNP-major mode
46
47Analysis finished: Wed May 19 15:15:38 2010
48