/test-data/rgtestouts/rgQC/rgQCtest1.html
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1<?xml version="1.0" encoding="utf-8" ?> 2<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 3<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 4<head> 5<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 6<meta name="generator" content="Galaxy rgQC.py tool output - see http://g2.trac.bx.psu.edu/" /> 7<title></title> 8<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 9</head> 10<body> 11<div class="document"> 12<h4> 13<div>Output from Rgenetics QC report tool run at 19/05/2010 15:15:46<br> 14</h4> 15</div><div><h4>(Click any preview image to download a full sized PDF version)</h4><br><ol> 16<table cellpadding="5" border="0"> 17<tr><td colspan="3"><a href="MarkerDetails_rgQCtest1.xls" type="application/vnd.ms-excel">Click here to download the Marker QC Detail report file</a> (1.4 KB) tab delimited</td></tr> 18<tr><td colspan="3"><a href="SubjectDetails_rgQCtest1.xls" type="application/vnd.ms-excel">Click here to download the Subject QC Detail report file</a> (1.4 KB) tab delimited</td></tr> 19<tr><td><a href="tinywga_All_Paged.pdf"><img src="tinywga_All_Paged-0.jpg" alt="All tinywga QC Plots joined into a single pdf" hspace="10" align="middle"> 20</a></td><td>All tinywga QC Plots joined into a single pdf</td><td> </td></tr> 21<tr><td><a href="tinywga_All_3x3.pdf"><img src="tinywga_All_3x3-0.jpg" alt="All tinywga QC Plots 3 by 3 to a page" hspace="10" align="middle"> 22</a></td><td>All tinywga QC Plots 3 by 3 to a page</td><td> </td></tr> 23<tr><td><a href="tinywga_logphweunaff.pdf"><img src="tinywga_logphweunaff.jpg" alt="Marker HWE" hspace="10" align="middle"> 24</a></td><td>Marker HWE</td><td><a href="Ranked_Marker_HWE.xls">Worst data</a></td></tr> 25<tr><td><a href="tinywga_logphweunaff_cum.pdf"><img src="tinywga_logphweunaff_cum.jpg" alt="Ranked Marker HWE" hspace="10" align="middle"> 26</a></td><td>Ranked Marker HWE</td><td> </td></tr> 27<tr><td><a href="QQtinywga_logphweunaff_cum.pdf"><img src="QQtinywga_logphweunaff_cum.jpg" alt="LogQQ plot Marker HWE" hspace="10" align="middle"> 28</a></td><td>LogQQ plot Marker HWE</td><td> </td></tr> 29<tr><td><a href="tinywga_missfrac.pdf"><img src="tinywga_missfrac.jpg" alt="Marker Missing Genotype" hspace="10" align="middle"> 30</a></td><td>Marker Missing Genotype</td><td><a href="Ranked_Marker_Missing_Genotype.xls">Worst data</a></td></tr> 31<tr><td><a href="tinywga_missfrac_cum.pdf"><img src="tinywga_missfrac_cum.jpg" alt="Ranked Marker Missing Genotype" hspace="10" align="middle"> 32</a></td><td>Ranked Marker Missing Genotype</td><td> </td></tr> 33<tr><td><a href="tinywga_maf.pdf"><img src="tinywga_maf.jpg" alt="Marker MAF" hspace="10" align="middle"> 34</a></td><td>Marker MAF</td><td><a href="Ranked_Marker_MAF.xls">Worst data</a></td></tr> 35<tr><td><a href="tinywga_maf_cum.pdf"><img src="tinywga_maf_cum.jpg" alt="Ranked Marker MAF" hspace="10" align="middle"> 36</a></td><td>Ranked Marker MAF</td><td> </td></tr> 37<tr><td><a href="tinywga_fracmiss.pdf"><img src="tinywga_fracmiss.jpg" alt="Subject Missing Genotype" hspace="10" align="middle"> 38</a></td><td>Subject Missing Genotype</td><td><a href="Ranked_Subject_Missing_Genotype.xls">Worst data</a></td></tr> 39<tr><td><a href="tinywga_fracmiss_cum.pdf"><img src="tinywga_fracmiss_cum.jpg" alt="Ranked Subject Missing Genotype" hspace="10" align="middle"> 40</a></td><td>Ranked Subject Missing Genotype</td><td> </td></tr> 41<tr><td><a href="tinywga_s_het.pdf"><img src="tinywga_s_het.jpg" alt="Subject F Statistic" hspace="10" align="middle"> 42</a></td><td>Subject F Statistic</td><td> </td></tr> 43<tr><td><a href="tinywga_s_het_cum.pdf"><img src="tinywga_s_het_cum.jpg" alt="Ranked Subject F Statistic" hspace="10" align="middle"> 44</a></td><td>Ranked Subject F Statistic</td><td> </td></tr> 45<tr><td><a href="FQNormtinywga_s_het_cum.pdf"><img src="FQNormtinywga_s_het_cum.jpg" alt="F Statistic Subject F Statistic" hspace="10" align="middle"> 46</a></td><td>F Statistic Subject F Statistic</td><td> </td></tr> 47</table><hr><h3>All output files from the QC run are available below</h3> 48<table cellpadding="5" border="0"> 49 50<tr><td><a href="FQNormtinywga_s_het_cum.jpg">FQNormtinywga_s_het_cum.jpg</a> (30.2 KB)</td></tr> 51<tr><td><a href="FQNormtinywga_s_het_cum.pdf">FQNormtinywga_s_het_cum.pdf</a> (7.1 KB)</td></tr> 52<tr><td><a href="MarkerDetails_rgQCtest1.xls">MarkerDetails_rgQCtest1.xls</a> (1.4 KB)</td></tr> 53<tr><td><a href="QQtinywga_logphweunaff_cum.jpg">QQtinywga_logphweunaff_cum.jpg</a> (33.0 KB)</td></tr> 54<tr><td><a href="QQtinywga_logphweunaff_cum.pdf">QQtinywga_logphweunaff_cum.pdf</a> (6.6 KB)</td></tr> 55<tr><td><a href="Ranked_Marker_HWE.xls">Ranked_Marker_HWE.xls</a> (763 B)</td></tr> 56<tr><td><a href="Ranked_Marker_MAF.xls">Ranked_Marker_MAF.xls</a> (564 B)</td></tr> 57<tr><td><a href="Ranked_Marker_Missing_Genotype.xls">Ranked_Marker_Missing_Genotype.xls</a> (659 B)</td></tr> 58<tr><td><a href="Ranked_Subject_Missing_Genotype.xls">Ranked_Subject_Missing_Genotype.xls</a> (804 B)</td></tr> 59<tr><td><a href="SubjectDetails_rgQCtest1.xls">SubjectDetails_rgQCtest1.xls</a> (1.4 KB)</td></tr> 60<tr><td><a href="ldp_tinywga.bed">ldp_tinywga.bed</a> (143 B)</td></tr> 61<tr><td><a href="ldp_tinywga.bim">ldp_tinywga.bim</a> (392 B)</td></tr> 62<tr><td><a href="ldp_tinywga.fam">ldp_tinywga.fam</a> (603 B)</td></tr> 63<tr><td><a href="ldp_tinywga.log">ldp_tinywga.log</a> (2.0 KB)</td></tr> 64<tr><td><a href="tinywga.fmendel">tinywga.fmendel</a> (378 B)</td></tr> 65<tr><td><a href="tinywga.frq">tinywga.frq</a> (1.2 KB)</td></tr> 66<tr><td><a href="tinywga.het">tinywga.het</a> (2.5 KB)</td></tr> 67<tr><td><a href="tinywga.hwe">tinywga.hwe</a> (6.5 KB)</td></tr> 68<tr><td><a href="tinywga.imendel">tinywga.imendel</a> (612 B)</td></tr> 69<tr><td><a href="tinywga.imiss">tinywga.imiss</a> (1.9 KB)</td></tr> 70<tr><td><a href="tinywga.lmendel">tinywga.lmendel</a> (571 B)</td></tr> 71<tr><td><a href="tinywga.lmiss">tinywga.lmiss</a> (1.1 KB)</td></tr> 72<tr><td><a href="tinywga.log">tinywga.log</a> (1.9 KB)</td></tr> 73<tr><td><a href="tinywga.mendel">tinywga.mendel</a> (56 B)</td></tr> 74<tr><td><a href="tinywga.prune.in">tinywga.prune.in</a> (140 B)</td></tr> 75<tr><td><a href="tinywga.prune.out">tinywga.prune.out</a> (110 B)</td></tr> 76<tr><td><a href="tinywga.sexcheck">tinywga.sexcheck</a> (2.5 KB)</td></tr> 77<tr><td><a href="tinywga_All_3x3-0.jpg">tinywga_All_3x3-0.jpg</a> (45.2 KB)</td></tr> 78<tr><td><a href="tinywga_All_3x3-1.jpg">tinywga_All_3x3-1.jpg</a> (19.3 KB)</td></tr> 79<tr><td><a href="tinywga_All_3x3.pdf">tinywga_All_3x3.pdf</a> (82.4 KB)</td></tr> 80<tr><td><a href="tinywga_All_Paged-0.jpg">tinywga_All_Paged-0.jpg</a> (13.6 KB)</td></tr> 81<tr><td><a href="tinywga_All_Paged-1.jpg">tinywga_All_Paged-1.jpg</a> (26.3 KB)</td></tr> 82<tr><td><a href="tinywga_All_Paged-10.jpg">tinywga_All_Paged-10.jpg</a> (31.4 KB)</td></tr> 83<tr><td><a href="tinywga_All_Paged-11.jpg">tinywga_All_Paged-11.jpg</a> (29.8 KB)</td></tr> 84<tr><td><a href="tinywga_All_Paged-2.jpg">tinywga_All_Paged-2.jpg</a> (32.3 KB)</td></tr> 85<tr><td><a href="tinywga_All_Paged-3.jpg">tinywga_All_Paged-3.jpg</a> (11.1 KB)</td></tr> 86<tr><td><a href="tinywga_All_Paged-4.jpg">tinywga_All_Paged-4.jpg</a> (26.7 KB)</td></tr> 87<tr><td><a href="tinywga_All_Paged-5.jpg">tinywga_All_Paged-5.jpg</a> (18.4 KB)</td></tr> 88<tr><td><a href="tinywga_All_Paged-6.jpg">tinywga_All_Paged-6.jpg</a> (28.1 KB)</td></tr> 89<tr><td><a href="tinywga_All_Paged-7.jpg">tinywga_All_Paged-7.jpg</a> (11.9 KB)</td></tr> 90<tr><td><a href="tinywga_All_Paged-8.jpg">tinywga_All_Paged-8.jpg</a> (29.6 KB)</td></tr> 91<tr><td><a href="tinywga_All_Paged-9.jpg">tinywga_All_Paged-9.jpg</a> (17.9 KB)</td></tr> 92<tr><td><a href="tinywga_All_Paged.pdf">tinywga_All_Paged.pdf</a> (81.9 KB)</td></tr> 93<tr><td><a href="tinywga_fracmiss.jpg">tinywga_fracmiss.jpg</a> (12.0 KB)</td></tr> 94<tr><td><a href="tinywga_fracmiss.pdf">tinywga_fracmiss.pdf</a> (6.4 KB)</td></tr> 95<tr><td><a href="tinywga_fracmiss_cum.jpg">tinywga_fracmiss_cum.jpg</a> (30.0 KB)</td></tr> 96<tr><td><a href="tinywga_fracmiss_cum.pdf">tinywga_fracmiss_cum.pdf</a> (7.0 KB)</td></tr> 97<tr><td><a href="tinywga_logphweunaff.jpg">tinywga_logphweunaff.jpg</a> (13.6 KB)</td></tr> 98<tr><td><a href="tinywga_logphweunaff.pdf">tinywga_logphweunaff.pdf</a> (5.7 KB)</td></tr> 99<tr><td><a href="tinywga_logphweunaff_cum.jpg">tinywga_logphweunaff_cum.jpg</a> (26.8 KB)</td></tr> 100<tr><td><a href="tinywga_logphweunaff_cum.pdf">tinywga_logphweunaff_cum.pdf</a> (5.8 KB)</td></tr> 101<tr><td><a href="tinywga_maf.jpg">tinywga_maf.jpg</a> (18.5 KB)</td></tr> 102<tr><td><a href="tinywga_maf.pdf">tinywga_maf.pdf</a> (6.4 KB)</td></tr> 103<tr><td><a href="tinywga_maf_cum.jpg">tinywga_maf_cum.jpg</a> (28.5 KB)</td></tr> 104<tr><td><a href="tinywga_maf_cum.pdf">tinywga_maf_cum.pdf</a> (6.0 KB)</td></tr> 105<tr><td><a href="tinywga_missfrac.jpg">tinywga_missfrac.jpg</a> (11.1 KB)</td></tr> 106<tr><td><a href="tinywga_missfrac.pdf">tinywga_missfrac.pdf</a> (5.9 KB)</td></tr> 107<tr><td><a href="tinywga_missfrac_cum.jpg">tinywga_missfrac_cum.jpg</a> (27.3 KB)</td></tr> 108<tr><td><a href="tinywga_missfrac_cum.pdf">tinywga_missfrac_cum.pdf</a> (5.9 KB)</td></tr> 109<tr><td><a href="tinywga_s_het.jpg">tinywga_s_het.jpg</a> (18.0 KB)</td></tr> 110<tr><td><a href="tinywga_s_het.pdf">tinywga_s_het.pdf</a> (6.8 KB)</td></tr> 111<tr><td><a href="tinywga_s_het_cum.jpg">tinywga_s_het_cum.jpg</a> (31.9 KB)</td></tr> 112<tr><td><a href="tinywga_s_het_cum.pdf">tinywga_s_het_cum.pdf</a> (7.3 KB)</td></tr> 113</table><h4>QC run log contents</h4><pre>## subject reports starting at 19/05/2010 15:15:38 114## imissfile /opt/galaxy/test-data/rgtestouts/rgQC/tinywga.imiss contained 40 ids 115### writing /opt/galaxy/test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls report with ['famId', 'iId', 'FracMiss', 'Mendel_errors', 'Ped_sex', 'SNP_sex', 'Status', 'XHomEst', 'F_Stat']## marker reports starting at 19/05/2010 15:15:38 116hwe header testpos=2,ppos=8,snppos=1 117## starting plotpage, newfpath=/opt/galaxy/test-data/rgtestouts/rgQC,m=[['snp', 'chromosome', 'offset', 'maf', 'a1', 'a2', 'missfrac', 'p_hwe_all', 'logp_hwe_all', 'p_hwe_unaff', 'logp_hwe_unaff', 'N_Mendel'], ['rs2283802', '22', '21784722', '0.2593', '4', '2', '0', '0.638', '0.195179', '0.638', '0.195179', '0']],s=[['famId', 'iId', 'FracMiss', 'Mendel_errors', 'Ped_sex', 'SNP_sex', 'Status', 'XHomEst', 'F_Stat'], ['101', '1', '0.04', '0', '2', '0', 'PROBLEM', 'nan', '-0.03355']]/n## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink runner 118 119@----------------------------------------------------------@ 120| PLINK! | v1.06 | 24/Apr/2009 | 121|----------------------------------------------------------| 122| (C) 2009 Shaun Purcell, GNU General Public License, v2 | 123|----------------------------------------------------------| 124| For documentation, citation & bug-report instructions: | 125| http://pngu.mgh.harvard.edu/purcell/plink/ | 126@----------------------------------------------------------@ 127 128Skipping web check... [ --noweb ] 129Writing this text to log file [ tinywga.log ] 130Analysis started: Wed May 19 15:15:38 2010 131 132Options in effect: 133 --noweb 134 --out tinywga 135 --bfile /opt/galaxy/test-data/tinywga 136 --mind 1.0 137 --geno 1.0 138 --maf 0.0 139 --freq 140 141Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 14225 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] 143Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 14440 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 14540 individuals with nonmissing phenotypes 146Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 147Missing phenotype value is also -9 14810 cases, 30 controls and 0 missing 14921 males, 19 females, and 0 of unspecified sex 150Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 151Detected that binary PED file is v1.00 SNP-major mode 152Before frequency and genotyping pruning, there are 25 SNPs 15327 founders and 13 non-founders found 154Writing allele frequencies (founders-only) to [ tinywga.frq ] 155 156Analysis finished: Wed May 19 15:15:38 2010 157 158 159@----------------------------------------------------------@ 160| PLINK! | v1.06 | 24/Apr/2009 | 161|----------------------------------------------------------| 162| (C) 2009 Shaun Purcell, GNU General Public License, v2 | 163|----------------------------------------------------------| 164| For documentation, citation & bug-report instructions: | 165| http://pngu.mgh.harvard.edu/purcell/plink/ | 166@----------------------------------------------------------@ 167 168Skipping web check... [ --noweb ] 169Writing this text to log file [ tinywga.log ] 170Analysis started: Wed May 19 15:15:38 2010 171 172Options in effect: 173 --noweb 174 --out tinywga 175 --bfile /opt/galaxy/test-data/tinywga 176 --mind 1.0 177 --geno 1.0 178 --maf 0.0 179 --hwe 0.0 180 --missing 181 --hardy 182 183Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 18425 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] 185Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 18640 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 18740 individuals with nonmissing phenotypes 188Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 189Missing phenotype value is also -9 19010 cases, 30 controls and 0 missing 19121 males, 19 females, and 0 of unspecified sex 192Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 193Detected that binary PED file is v1.00 SNP-major mode 194Before frequency and genotyping pruning, there are 25 SNPs 19527 founders and 13 non-founders found 196Writing Hardy-Weinberg tests (founders-only) to [ tinywga.hwe ] 1970 markers to be excluded based on HWE test ( p <= 0 ) 198 0 markers failed HWE test in cases 199 0 markers failed HWE test in controls 200Writing individual missingness information to [ tinywga.imiss ] 201Writing locus missingness information to [ tinywga.lmiss ] 202Total genotyping rate in remaining individuals is 0.995 2030 SNPs failed missingness test ( GENO > 1 ) 2040 SNPs failed frequency test ( MAF < 0 ) 205After frequency and genotyping pruning, there are 25 SNPs 206After filtering, 10 cases, 30 controls and 0 missing 207After filtering, 21 males, 19 females, and 0 of unspecified sex 208 209Analysis finished: Wed May 19 15:15:38 2010 210 211 212@----------------------------------------------------------@ 213| PLINK! | v1.06 | 24/Apr/2009 | 214|----------------------------------------------------------| 215| (C) 2009 Shaun Purcell, GNU General Public License, v2 | 216|----------------------------------------------------------| 217| For documentation, citation & bug-report instructions: | 218| http://pngu.mgh.harvard.edu/purcell/plink/ | 219@----------------------------------------------------------@ 220 221Skipping web check... [ --noweb ] 222Writing this text to log file [ tinywga.log ] 223Analysis started: Wed May 19 15:15:38 2010 224 225Options in effect: 226 --noweb 227 --out tinywga 228 --bfile /opt/galaxy/test-data/tinywga 229 --mind 1.0 230 --geno 1.0 231 --maf 0.0 232 --mendel 233 234Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 23525 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] 236Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 23740 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 23840 individuals with nonmissing phenotypes 239Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 240Missing phenotype value is also -9 24110 cases, 30 controls and 0 missing 24221 males, 19 females, and 0 of unspecified sex 243Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 244Detected that binary PED file is v1.00 SNP-major mode 245Before frequency and genotyping pruning, there are 25 SNPs 24627 founders and 13 non-founders found 247Total genotyping rate in remaining individuals is 0.995 2480 SNPs failed missingness test ( GENO > 1 ) 2490 SNPs failed frequency test ( MAF < 0 ) 250After frequency and genotyping pruning, there are 25 SNPs 251After filtering, 10 cases, 30 controls and 0 missing 252After filtering, 21 males, 19 females, and 0 of unspecified sex 25314 nuclear families, 1 founder singletons found 25413 non-founders with 2 parents in 13 nuclear families 2550 non-founders without 2 parents in 0 nuclear families 25610 affected offspring trios 2570 phenotypically discordant parent pairs found 258Converting data to Individual-major format 259Writing all Mendel errors to [ tinywga.mendel ] 260Writing per-offspring Mendel summary to [ tinywga.imendel ] 261Writing per-family Mendel summary to [ tinywga.fmendel ] 262Writing per-locus Mendel summary to [ tinywga.lmendel ] 2630 Mendel errors detected in total 264 265Analysis finished: Wed May 19 15:15:38 2010 266 267 268@----------------------------------------------------------@ 269| PLINK! | v1.06 | 24/Apr/2009 | 270|----------------------------------------------------------| 271| (C) 2009 Shaun Purcell, GNU General Public License, v2 | 272|----------------------------------------------------------| 273| For documentation, citation & bug-report instructions: | 274| http://pngu.mgh.harvard.edu/purcell/plink/ | 275@----------------------------------------------------------@ 276 277Skipping web check... [ --noweb ] 278Writing this text to log file [ tinywga.log ] 279Analysis started: Wed May 19 15:15:38 2010 280 281Options in effect: 282 --noweb 283 --out tinywga 284 --bfile /opt/galaxy/test-data/tinywga 285 --mind 1.0 286 --geno 1.0 287 --maf 0.0 288 --check-sex 289 290Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 29125 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] 292Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 29340 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 29440 individuals with nonmissing phenotypes 295Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 296Missing phenotype value is also -9 29710 cases, 30 controls and 0 missing 29821 males, 19 females, and 0 of unspecified sex 299Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 300Detected that binary PED file is v1.00 SNP-major mode 301Before frequency and genotyping pruning, there are 25 SNPs 30227 founders and 13 non-founders found 303Total genotyping rate in remaining individuals is 0.995 3040 SNPs failed missingness test ( GENO > 1 ) 3050 SNPs failed frequency test ( MAF < 0 ) 306After frequency and genotyping pruning, there are 25 SNPs 307After filtering, 10 cases, 30 controls and 0 missing 308After filtering, 21 males, 19 females, and 0 of unspecified sex 309Converting data to Individual-major format 310Writing X-chromosome sex check results to [ tinywga.sexcheck ] 311 312Analysis finished: Wed May 19 15:15:38 2010 313 314## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner 315 316 317 318@----------------------------------------------------------@ 319 320| PLINK! | v1.06 | 24/Apr/2009 | 321 322|----------------------------------------------------------| 323 324| (C) 2009 Shaun Purcell, GNU General Public License, v2 | 325 326|----------------------------------------------------------| 327 328| For documentation, citation & bug-report instructions: | 329 330| http://pngu.mgh.harvard.edu/purcell/plink/ | 331 332@----------------------------------------------------------@ 333 334 335 336Skipping web check... [ --noweb ] 337 338Writing this text to log file [ tinywga.log ] 339 340Analysis started: Wed May 19 15:15:38 2010 341 342 343 344Options in effect: 345 346 --noweb 347 348 --bfile /opt/galaxy/test-data/tinywga 349 350 --indep-pairwise 40 20 0.5 351 352 --out tinywga 353 354 355 356Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 357 35825 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] 359 360Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 361 36240 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 363 36440 individuals with nonmissing phenotypes 365 366Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 367 368Missing phenotype value is also -9 369 37010 cases, 30 controls and 0 missing 371 37221 males, 19 females, and 0 of unspecified sex 373 374Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 375 376Detected that binary PED file is v1.00 SNP-major mode 377 378Before frequency and genotyping pruning, there are 25 SNPs 379 38027 founders and 13 non-founders found 381 382Total genotyping rate in remaining individuals is 0.995 383 3840 SNPs failed missingness test ( GENO > 1 ) 385 3860 SNPs failed frequency test ( MAF < 0 ) 387 388After frequency and genotyping pruning, there are 25 SNPs 389 390After filtering, 10 cases, 30 controls and 0 missing 391 392After filtering, 21 males, 19 females, and 0 of unspecified sex 393 394Performing LD-based pruning... 395 396Writing pruned-in SNPs to [ tinywga.prune.in ] 397 398Writing pruned-out SNPs to [ tinywga.prune.out ] 399 400Scanning from chromosome 22 to 22 401 402 403 404Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ] 405 406For chromosome 22, 11 SNPs pruned out, 14 remaining 407 408 409 410Analysis finished: Wed May 19 15:15:38 2010 411 412 413 414 415 416 417 418@----------------------------------------------------------@ 419 420| PLINK! | v1.06 | 24/Apr/2009 | 421 422|----------------------------------------------------------| 423 424| (C) 2009 Shaun Purcell, GNU General Public License, v2 | 425 426|----------------------------------------------------------| 427 428| For documentation, citation & bug-report instructions: | 429 430| http://pngu.mgh.harvard.edu/purcell/plink/ | 431 432@----------------------------------------------------------@ 433 434 435 436Skipping web check... [ --noweb ] 437 438Writing this text to log file [ ldp_tinywga.log ] 439 440Analysis started: Wed May 19 15:15:38 2010 441 442 443 444Options in effect: 445 446 --noweb 447 448 --bfile /opt/galaxy/test-data/tinywga 449 450 --extract tinywga.prune.in 451 452 --make-bed 453 454 --out ldp_tinywga 455 456 457 458Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 459 46025 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] 461 462Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 463 46440 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 465 46640 individuals with nonmissing phenotypes 467 468Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 469 470Missing phenotype value is also -9 471 47210 cases, 30 controls and 0 missing 473 47421 males, 19 females, and 0 of unspecified sex 475 476Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 477 478Detected that binary PED file is v1.00 SNP-major mode 479 480Reading list of SNPs to extract [ tinywga.prune.in ] ... 14 read 481 482Before frequency and genotyping pruning, there are 14 SNPs 483 48427 founders and 13 non-founders found 485 486Total genotyping rate in remaining individuals is 0.991071 487 4880 SNPs failed missingness test ( GENO > 1 ) 489 4900 SNPs failed frequency test ( MAF < 0 ) 491 492After frequency and genotyping pruning, there are 14 SNPs 493 494After filtering, 10 cases, 30 controls and 0 missing 495 496After filtering, 21 males, 19 females, and 0 of unspecified sex 497 498Writing pedigree information to [ ldp_tinywga.fam ] 499 500Writing map (extended format) information to [ ldp_tinywga.bim ] 501 502Writing genotype bitfile to [ ldp_tinywga.bed ] 503 504Using (default) SNP-major mode 505 506 507 508Analysis finished: Wed May 19 15:15:38 2010 509 510 511 512 513 514 515 516@----------------------------------------------------------@ 517 518| PLINK! | v1.06 | 24/Apr/2009 | 519 520|----------------------------------------------------------| 521 522| (C) 2009 Shaun Purcell, GNU General Public License, v2 | 523 524|----------------------------------------------------------| 525 526| For documentation, citation & bug-report instructions: | 527 528| http://pngu.mgh.harvard.edu/purcell/plink/ | 529 530@----------------------------------------------------------@ 531 532 533 534Skipping web check... [ --noweb ] 535 536Writing this text to log file [ tinywga.log ] 537 538Analysis started: Wed May 19 15:15:38 2010 539 540 541 542Options in effect: 543 544 --noweb 545 546 --bfile ldp_tinywga 547 548 --het 549 550 --out tinywga 551 552 553 554Reading map (extended format) from [ ldp_tinywga.bim ] 555 55614 markers to be included from [ ldp_tinywga.bim ] 557 558Reading pedigree information from [ ldp_tinywga.fam ] 559 56040 individuals read from [ ldp_tinywga.fam ] 561 56240 individuals with nonmissing phenotypes 563 564Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 565 566Missing phenotype value is also -9 567 56810 cases, 30 controls and 0 missing 569 57021 males, 19 females, and 0 of unspecified sex 571 572Reading genotype bitfile from [ ldp_tinywga.bed ] 573 574Detected that binary PED file is v1.00 SNP-major mode 575 576Before frequency and genotyping pruning, there are 14 SNPs 577 57827 founders and 13 non-founders found 579 580Total genotyping rate in remaining individuals is 0.991071 581 5820 SNPs failed missingness test ( GENO > 1 ) 583 5840 SNPs failed frequency test ( MAF < 0 ) 585 586After frequency and genotyping pruning, there are 14 SNPs 587 588After filtering, 10 cases, 30 controls and 0 missing 589 590After filtering, 21 males, 19 females, and 0 of unspecified sex 591 592 593 594 **Warning** this analysis typically requires whole-genome level data 595 596 to give accurate results 597 598 599 600Converting data to Individual-major format 601 602Writing individual heterozygosity information to [ tinywga.het ] 603 604 605 606Analysis finished: Wed May 19 15:15:38 2010 607 608 609 610 611 612</pre></div></body></html> 613 614<hr>