[2] | 1 | |
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| 2 | @----------------------------------------------------------@ |
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| 3 | | PLINK! | v1.06 | 24/Apr/2009 | |
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| 4 | |----------------------------------------------------------| |
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| 5 | | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |
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| 6 | |----------------------------------------------------------| |
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| 7 | | For documentation, citation & bug-report instructions: | |
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| 8 | | http://pngu.mgh.harvard.edu/purcell/plink/ | |
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| 9 | @----------------------------------------------------------@ |
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| 10 | |
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| 11 | Skipping web check... [ --noweb ] |
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| 12 | Writing this text to log file [ ldp_tinywga.log ] |
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| 13 | Analysis started: Wed May 19 15:15:38 2010 |
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| 14 | |
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| 15 | Options in effect: |
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| 16 | --noweb |
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| 17 | --bfile /opt/galaxy/test-data/tinywga |
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| 18 | --extract tinywga.prune.in |
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| 19 | --make-bed |
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| 20 | --out ldp_tinywga |
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| 21 | |
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| 22 | Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] |
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| 23 | 25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] |
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| 24 | Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] |
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| 25 | 40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] |
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| 26 | 40 individuals with nonmissing phenotypes |
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| 27 | Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) |
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| 28 | Missing phenotype value is also -9 |
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| 29 | 10 cases, 30 controls and 0 missing |
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| 30 | 21 males, 19 females, and 0 of unspecified sex |
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| 31 | Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] |
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| 32 | Detected that binary PED file is v1.00 SNP-major mode |
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| 33 | Reading list of SNPs to extract [ tinywga.prune.in ] ... 14 read |
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| 34 | Before frequency and genotyping pruning, there are 14 SNPs |
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| 35 | 27 founders and 13 non-founders found |
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| 36 | Total genotyping rate in remaining individuals is 0.991071 |
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| 37 | 0 SNPs failed missingness test ( GENO > 1 ) |
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| 38 | 0 SNPs failed frequency test ( MAF < 0 ) |
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| 39 | After frequency and genotyping pruning, there are 14 SNPs |
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| 40 | After filtering, 10 cases, 30 controls and 0 missing |
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| 41 | After filtering, 21 males, 19 females, and 0 of unspecified sex |
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| 42 | Writing pedigree information to [ ldp_tinywga.fam ] |
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| 43 | Writing map (extended format) information to [ ldp_tinywga.bim ] |
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| 44 | Writing genotype bitfile to [ ldp_tinywga.bed ] |
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| 45 | Using (default) SNP-major mode |
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| 46 | |
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| 47 | Analysis finished: Wed May 19 15:15:38 2010 |
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| 48 | |
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