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/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log

https://bitbucket.org/cistrome/cistrome-harvard/
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  1## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 09/05/2010 21:23:42
  2## Rgenetics January 4 2010: http://rgenetics.org Galaxy Tools rgLDIndep.py Plink pruneLD runner
  3## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1
  4
  5@----------------------------------------------------------@
  6|        PLINK!       |     v1.07      |   10/Aug/2009     |
  7|----------------------------------------------------------|
  8|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
  9|----------------------------------------------------------|
 10|  For documentation, citation & bug-report instructions:  |
 11|        http://pngu.mgh.harvard.edu/purcell/plink/        |
 12@----------------------------------------------------------@
 13
 14Skipping web check... [ --noweb ] 
 15Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ]
 16Analysis started: Sun May  9 21:23:42 2010
 17
 18Options in effect:
 19	--noweb
 20	--bfile /share/shared/galaxy/test-data/tinywga
 21	--indep-pairwise 10000 5000 0.1
 22	--out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
 23	--mind 1
 24	--geno 1
 25	--maf 0
 26	--hwe 0
 27	--me 1 1
 28
 29Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
 3025 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
 31Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
 3240 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
 3340 individuals with nonmissing phenotypes
 34Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
 35Missing phenotype value is also -9
 3610 cases, 30 controls and 0 missing
 3721 males, 19 females, and 0 of unspecified sex
 38Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
 39Detected that binary PED file is v1.00 SNP-major mode
 40Before frequency and genotyping pruning, there are 25 SNPs
 4127 founders and 13 non-founders found
 420 markers to be excluded based on HWE test ( p <= 0 )
 43	0 markers failed HWE test in cases
 44	0 markers failed HWE test in controls
 45Total genotyping rate in remaining individuals is 0.995
 460 SNPs failed missingness test ( GENO > 1 )
 470 SNPs failed frequency test ( MAF < 0 )
 48After frequency and genotyping pruning, there are 25 SNPs
 49After filtering, 10 cases, 30 controls and 0 missing
 50After filtering, 21 males, 19 females, and 0 of unspecified sex
 5114 nuclear families, 1 founder singletons found
 5213 non-founders with 2 parents in 13 nuclear families
 530 non-founders without 2 parents in 0 nuclear families
 5410 affected offspring trios
 550 phenotypically discordant parent pairs found
 56Converting data to Individual-major format
 57Filtering SNPs/families for Mendel Error rates above 1, 1
 580 Mendel errors detected in total
 590 families ( 0 individuals ) removed due to Mendel errors
 600 markers removed due to Mendel errors, 25 remaining
 61Converting data to SNP-major format
 62Performing LD-based pruning...
 63Writing pruned-in SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ]
 64Writing pruned-out SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ]
 65Scanning from chromosome 22 to 22
 66
 67Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ]
 68For chromosome 22, 22 SNPs pruned out, 3 remaining
 69
 70Analysis finished: Sun May  9 21:23:42 2010
 71
 72
 73## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/tinywga --extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
 74
 75@----------------------------------------------------------@
 76|        PLINK!       |     v1.07      |   10/Aug/2009     |
 77|----------------------------------------------------------|
 78|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
 79|----------------------------------------------------------|
 80|  For documentation, citation & bug-report instructions:  |
 81|        http://pngu.mgh.harvard.edu/purcell/plink/        |
 82@----------------------------------------------------------@
 83
 84Skipping web check... [ --noweb ] 
 85Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ]
 86Analysis started: Sun May  9 21:23:42 2010
 87
 88Options in effect:
 89	--noweb
 90	--bfile /share/shared/galaxy/test-data/tinywga
 91	--extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in
 92	--make-bed
 93	--out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
 94
 95Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] 
 9625 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ]
 97Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] 
 9840 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 
 9940 individuals with nonmissing phenotypes
100Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
101Missing phenotype value is also -9
10210 cases, 30 controls and 0 missing
10321 males, 19 females, and 0 of unspecified sex
104Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] 
105Detected that binary PED file is v1.00 SNP-major mode
106Reading list of SNPs to extract [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read
107Before frequency and genotyping pruning, there are 3 SNPs
10827 founders and 13 non-founders found
109Total genotyping rate in remaining individuals is 1
1100 SNPs failed missingness test ( GENO > 1 )
1110 SNPs failed frequency test ( MAF < 0 )
112After frequency and genotyping pruning, there are 3 SNPs
113After filtering, 10 cases, 30 controls and 0 missing
114After filtering, 21 males, 19 females, and 0 of unspecified sex
115Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 
116Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] 
117Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] 
118Using (default) SNP-major mode
119
120Analysis finished: Sun May  9 21:23:42 2010
121
122
123## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
124
125@----------------------------------------------------------@
126|        PLINK!       |     v1.07      |   10/Aug/2009     |
127|----------------------------------------------------------|
128|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
129|----------------------------------------------------------|
130|  For documentation, citation & bug-report instructions:  |
131|        http://pngu.mgh.harvard.edu/purcell/plink/        |
132@----------------------------------------------------------@
133
134Skipping web check... [ --noweb ] 
135Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ]
136Analysis started: Sun May  9 21:23:42 2010
137
138Options in effect:
139	--noweb
140	--bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
141	--recode
142	--out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1
143
144Reading map (extended format) from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] 
1453 markers to be included from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ]
146Reading pedigree information from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 
14740 individuals read from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 
14840 individuals with nonmissing phenotypes
149Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
150Missing phenotype value is also -9
15110 cases, 30 controls and 0 missing
15221 males, 19 females, and 0 of unspecified sex
153Reading genotype bitfile from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] 
154Detected that binary PED file is v1.00 SNP-major mode
155Before frequency and genotyping pruning, there are 3 SNPs
15627 founders and 13 non-founders found
157Total genotyping rate in remaining individuals is 1
1580 SNPs failed missingness test ( GENO > 1 )
1590 SNPs failed frequency test ( MAF < 0 )
160After frequency and genotyping pruning, there are 3 SNPs
161After filtering, 10 cases, 30 controls and 0 missing
162After filtering, 21 males, 19 females, and 0 of unspecified sex
163Writing recoded ped file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] 
164Writing new map file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] 
165
166Analysis finished: Sun May  9 21:23:42 2010
167
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