[2] | 1 | 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 |
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| 2 | |
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| 3 | @----------------------------------------------------------@ |
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| 4 | | PLINK! | v1.07 | 10/Aug/2009 | |
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| 5 | |----------------------------------------------------------| |
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| 6 | | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |
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| 7 | |----------------------------------------------------------| |
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| 8 | | For documentation, citation & bug-report instructions: | |
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| 9 | | http://pngu.mgh.harvard.edu/purcell/plink/ | |
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| 10 | @----------------------------------------------------------@ |
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| 11 | |
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| 12 | Skipping web check... [ --noweb ] |
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| 13 | Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ] |
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| 14 | Analysis started: Sun May 9 21:23:43 2010 |
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| 15 | |
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| 16 | Options in effect: |
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| 17 | --noweb |
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| 18 | --bfile /share/shared/galaxy/test-data/tinywga |
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| 19 | --make-bed |
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| 20 | --out /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1 |
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| 21 | --set-hh-missing |
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| 22 | --mind 1 |
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| 23 | --geno 1 |
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| 24 | --maf 0 |
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| 25 | --hwe 0 |
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| 26 | --me 1 1 |
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| 27 | |
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| 28 | Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] |
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| 29 | 25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] |
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| 30 | Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] |
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| 31 | 40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] |
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| 32 | 40 individuals with nonmissing phenotypes |
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| 33 | Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) |
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| 34 | Missing phenotype value is also -9 |
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| 35 | 10 cases, 30 controls and 0 missing |
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| 36 | 21 males, 19 females, and 0 of unspecified sex |
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| 37 | Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] |
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| 38 | Detected that binary PED file is v1.00 SNP-major mode |
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| 39 | Before frequency and genotyping pruning, there are 25 SNPs |
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| 40 | 27 founders and 13 non-founders found |
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| 41 | 0 markers to be excluded based on HWE test ( p <= 0 ) |
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| 42 | 0 markers failed HWE test in cases |
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| 43 | 0 markers failed HWE test in controls |
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| 44 | Total genotyping rate in remaining individuals is 0.995 |
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| 45 | 0 SNPs failed missingness test ( GENO > 1 ) |
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| 46 | 0 SNPs failed frequency test ( MAF < 0 ) |
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| 47 | After frequency and genotyping pruning, there are 25 SNPs |
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| 48 | After filtering, 10 cases, 30 controls and 0 missing |
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| 49 | After filtering, 21 males, 19 females, and 0 of unspecified sex |
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| 50 | 14 nuclear families, 1 founder singletons found |
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| 51 | 13 non-founders with 2 parents in 13 nuclear families |
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| 52 | 0 non-founders without 2 parents in 0 nuclear families |
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| 53 | 10 affected offspring trios |
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| 54 | 0 phenotypically discordant parent pairs found |
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| 55 | Converting data to Individual-major format |
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| 56 | Filtering SNPs/families for Mendel Error rates above 1, 1 |
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| 57 | 0 Mendel errors detected in total |
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| 58 | 0 families ( 0 individuals ) removed due to Mendel errors |
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| 59 | 0 markers removed due to Mendel errors, 25 remaining |
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| 60 | Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ] |
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| 61 | Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ] |
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| 62 | Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ] |
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| 63 | Using (default) SNP-major mode |
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| 64 | Converting data to SNP-major format |
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| 65 | |
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| 66 | Analysis finished: Sun May 9 21:23:43 2010 |
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