[hg] galaxy 3759: SNP/WGA tool changes only
endobj 9 0 obj @@ -370,9 +402,9 @@ 0000000293 00000 n 0000006405 00000 n 0000006612 00000 n -0000006869 00000 n -0000006952 00000 n -0000007049 00000 n +0000009405 00000 n +0000009488 00000 n +0000009585 00000 n
details: http://www.bx.psu.edu/hg/galaxy/rev/6aa1379d35e0 changeset: 3759:6aa1379d35e0 user: fubar/ross period lazarus at gmail d0t com date: Mon May 10 10:17:11 2010 -0400 description: SNP/WGA tool changes only Updates to functional test outputs Minor tweaks to some tests All now pass when run using -sid but there's something busted when a full functional test is run diffstat: static/welcome.html | 5 +- test-data/rgCaCotest1_CaCo_log.txt | 20 +- test-data/rgGLMtest1_GLM_log.txt | 28 +- test-data/rgQQtest1.pdf | 52 +- test-data/rgTDTtest1_TDT_log.txt | 18 +- test-data/rgtestouts/rgClean/rgCleantest1.log | 28 +- test-data/rgtestouts/rgEigPCA/Rplots.pdf | 46 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R | 2 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html | 35 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf | 50 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt | 6 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls | 80 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par | 6 +- test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt | 8 +- test-data/rgtestouts/rgGRR/rgGRRtest1.html | 14 +- test-data/rgtestouts/rgGRR/rgGRRtest1.svg | 118 +- test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls | 1560 +++++----- test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf | 0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png | 0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf | 0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png | 0 test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG | 0 test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt | 16 +- test-data/rgtestouts/rgHaploView/alljoin.pdf | 0 test-data/rgtestouts/rgHaploView/allnup.pdf | 0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html | 16 +- test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG | 0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS | 14 +- test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS | 10 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed | 2 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim | 4 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log | 96 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map | 4 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped | 80 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in | 4 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out | 4 +- test-data/rgtestouts/rgManQQ/Allelep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/Allelep_qqplot.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png | 0 test-data/rgtestouts/rgManQQ/rgManQQtest1.R | 4 +- test-data/rgtestouts/rgManQQ/rgManQQtest1.html | 4 +- test-data/rgtestouts/rgPedSub/rgPedSubtest1.log | 8 +- test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.jpg | 0 test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.pdf | 182 +- test-data/rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls | 36 +- test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls | 72 +- test-data/rgtestouts/rgQC/ldp_tinywga.bed | 2 +- test-data/rgtestouts/rgQC/ldp_tinywga.bim | 10 +- test-data/rgtestouts/rgQC/ldp_tinywga.log | 18 +- test-data/rgtestouts/rgQC/rgQCtest1.html | 208 +- test-data/rgtestouts/rgQC/tinywga.het | 80 +- test-data/rgtestouts/rgQC/tinywga.log | 6 +- test-data/rgtestouts/rgQC/tinywga.prune.in | 10 +- test-data/rgtestouts/rgQC/tinywga.prune.out | 10 +- test-data/rgtestouts/rgQC/tinywga_All_3x3.pdf | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-0.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-1.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-2.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-3.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-4.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged.pdf | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss.jpg | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss.pdf | 50 +- test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.jpg | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.pdf | 52 +- test-data/rgtestouts/rgQC/tinywga_s_het.jpg | 0 test-data/rgtestouts/rgQC/tinywga_s_het.pdf | 343 +- test-data/rgtestouts/rgQC/tinywga_s_het_cum.jpg | 0 test-data/rgtestouts/rgQC/tinywga_s_het_cum.pdf | 182 +- test-data/rgtestouts/rgfakePed/rgfakePedtest1.lped | 2 +- test-data/rgtestouts/rgfakePed/rgfakePedtest1.ped | 80 +- test-data/rgtestouts/rgfakePhe/rgfakePhetest1.pphe | 80 +- tool-data/annotation_profiler_options.xml.sample | 2 +- tool_conf.xml.sample | 231 - tools/rgenetics/rgGRR.py | 12 +- tools/rgenetics/rgGRR.xml | 10 +- tools/rgenetics/rgHaploView.xml | 4 +- tools/rgenetics/rgQC.xml | 2 +- tools/rgenetics/rgtest.sh | 6 +- tools/rgenetics/rgutils.py | 20 +- 81 files changed, 2045 insertions(+), 2007 deletions(-) diffs (truncated from 5750 to 3000 lines): diff -r acaf971320bd -r 6aa1379d35e0 static/welcome.html --- a/static/welcome.html Mon May 10 10:03:00 2010 -0400 +++ b/static/welcome.html Mon May 10 10:17:11 2010 -0400 @@ -8,12 +8,11 @@ <body> <div class="document"> <div class="warningmessagelarge"> - <strong>Hello world! It's running...</strong> + <strong>Welcome to Galaxy at the Channing Laboratory</strong> <hr> - To customize this page edit <code>static/welcome.html</code> </div> <br/> - <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> + <img src="images/Armitagep_manhattan.png" alt="manhattan plot" style="display: block; margin-left: auto; margin-right: auto;" /> <hr/> This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. </div> diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgCaCotest1_CaCo_log.txt --- a/test-data/rgCaCotest1_CaCo_log.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgCaCotest1_CaCo_log.txt Mon May 10 10:17:11 2010 -0400 @@ -1,6 +1,6 @@ @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -10,24 +10,24 @@ Skipping web check... [ --noweb ] Writing this text to log file [ rgCaCotest1.log ] -Analysis started: Thu Mar 25 21:01:31 2010 +Analysis started: Sun May 9 21:23:49 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga + --bfile /share/shared/galaxy/test-data/tinywga --out rgCaCotest1 --model -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 25 SNPs 27 founders and 13 non-founders found @@ -40,7 +40,7 @@ Full-model association tests, minimum genotype count: --cell 5 Writing full model association results to [ rgCaCotest1.model ] -Analysis finished: Thu Mar 25 21:01:31 2010 +Analysis finished: Sun May 9 21:23:49 2010 ###maxp=0.667360,minp=-0.000000,prange=1.167360,scalefact=856.633772 -Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 25/03/2010 21:01:31 +Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 09/05/2010 21:23:49 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgGLMtest1_GLM_log.txt --- a/test-data/rgGLMtest1_GLM_log.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgGLMtest1_GLM_log.txt Mon May 10 10:17:11 2010 -0400 @@ -1,11 +1,11 @@ -rgGLM.py called with ['/opt/galaxy/tools/rgenetics/rgGLM.py', '/opt/galaxy/test-data/tinywga', '/opt/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/opt/galaxy/test-data/rgGLMtest1_GLM.xls', '/opt/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/opt/galaxy/test-data/rgGLM_GLM_topTable.gff'] -vcl=['plink', '--noweb', '--bfile', '/opt/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/opt/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear'] -xformQassoc got resf=/tmp/tmpCB6CwWrgGLM/tinywga.assoc.linear, outfname=/opt/galaxy/test-data/rgGLMtest1_GLM.xls +rgGLM.py called with ['/share/shared/galaxy/tools/rgenetics/rgGLM.py', '/share/shared/galaxy/test-data/tinywga', '/share/shared/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls', '/share/shared/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/share/shared/galaxy/test-data/rgGLMtest1_GLM_topTable.gff'] +vcl=['plink', '--noweb', '--bfile', '/share/shared/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/share/shared/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear'] +xformQassoc got resf=/tmp/tmpXKEn_LrgGLM/tinywga.assoc.linear, outfname=/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls ###maxp=1.188425,minp=0.046772,prange=1.641653,scalefact=609.142127 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -15,31 +15,31 @@ Skipping web check... [ --noweb ] Writing this text to log file [ tinywga.log ] -Analysis started: Thu Mar 25 21:01:31 2010 +Analysis started: Sun May 9 21:23:49 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga + --bfile /share/shared/galaxy/test-data/tinywga --pheno-name c1 - --pheno /opt/galaxy/test-data/tinywga.pphe + --pheno /share/shared/galaxy/test-data/tinywga.pphe --out tinywga --mind 1 --geno 1 --maf 0 --linear -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode -Reading alternate phenotype from [ /opt/galaxy/test-data/tinywga.pphe ] +Reading alternate phenotype from [ /share/shared/galaxy/test-data/tinywga.pphe ] 40 individuals with non-missing alternate phenotype Assuming a quantitative trait Missing phenotype value is -9 @@ -54,5 +54,5 @@ Converting data to Individual-major format Writing linear model association results to [ tinywga.assoc.linear ] -Analysis finished: Thu Mar 25 21:01:31 2010 +Analysis finished: Sun May 9 21:23:49 2010 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgQQtest1.pdf --- a/test-data/rgQQtest1.pdf Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgQQtest1.pdf Mon May 10 10:17:11 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210132) -/ModDate (D:20100325210132) +/CreationDate (D:20100509212350) +/ModDate (D:20100509212350) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) @@ -331,10 +331,42 @@ 8 0 obj << /Type /Encoding -/BaseEncoding /WinAnsiEncoding -/Differences [ 45/minus 96/quoteleft -144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent -/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +/BaseEncoding /PDFDocEncoding +/Differences [ + 0/.notdef 1/.notdef 2/.notdef 3/.notdef 4/.notdef 5/.notdef 6/.notdef 7/.notdef + 8/.notdef 9/.notdef 10/.notdef 11/.notdef 12/.notdef 13/.notdef 14/.notdef 15/.notdef + 16/.notdef 17/.notdef 18/.notdef 19/.notdef 20/.notdef 21/.notdef 22/.notdef 23/.notdef + 24/.notdef 25/.notdef 26/.notdef 27/.notdef 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220/Udieresis 221/Yacute 222/Thorn 223/germandbls + 224/agrave 225/aacute 226/acircumflex 227/atilde 228/adieresis 229/aring 230/ae 231/ccedilla + 232/egrave 233/eacute 234/ecircumflex 235/edieresis 236/igrave 237/iacute 238/icircumflex 239/idieresis + 240/eth 241/ntilde 242/ograve 243/oacute 244/ocircumflex 245/otilde 246/odieresis 247/divide + 248/oslash 249/ugrave 250/uacute 251/ucircumflex 252/udieresis 253/yacute 254/thorn 255/ydieresis + +] trailer << /Size 12 @@ -380,5 +412,5 @@ /Root 2 0 R
startxref -7151 +9687 %%EOF diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgTDTtest1_TDT_log.txt --- a/test-data/rgTDTtest1_TDT_log.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgTDTtest1_TDT_log.txt Mon May 10 10:17:11 2010 -0400 @@ -1,6 +1,6 @@
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startxref -618 +3154 %%EOF diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R Mon May 10 10:17:11 2010 -0400 @@ -16,4 +16,4 @@
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startxref -7818 +10354 %%EOF diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt Mon May 10 10:17:11 2010 -0400 @@ -1,9 +1,9 @@
@----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -10,25 +10,25 @@ Skipping web check... [ --noweb ] Writing this text to log file [ rgTDTtest1.log ] -Analysis started: Thu Mar 25 21:01:31 2010 +Analysis started: Sun May 9 21:23:49 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga + --bfile /share/shared/galaxy/test-data/tinywga --out rgTDTtest1 --mind 0.5 --tdt -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 25 SNPs 27 founders and 13 non-founders found @@ -48,6 +48,6 @@ 0 Mendel errors detected in total Writing TDT results (asymptotic) to [ rgTDTtest1.tdt ] -Analysis finished: Thu Mar 25 21:01:31 2010 +Analysis finished: Sun May 9 21:23:49 2010 ###maxp=0.590405,minp=-0.000000,prange=1.090405,scalefact=917.090439 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgClean/rgCleantest1.log --- a/test-data/rgtestouts/rgClean/rgCleantest1.log Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.log Mon May 10 10:17:11 2010 -0400 @@ -1,7 +1,7 @@ -rgClean.py started, called as /opt/galaxy/tools/rgenetics/rgClean.py /opt/galaxy/test-data tinywga rgCleantest1 1 1 0 0 1 1 /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.pbed /opt/galaxy/test-data/rgtestouts/rgClean 0 0 0 0 +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 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -10,14 +10,14 @@ @----------------------------------------------------------@ Skipping web check... [ --noweb ] -Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ] -Analysis started: Thu Mar 25 21:01:24 2010 +Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ] +Analysis started: Sun May 9 21:23:43 2010 Options in effect: --noweb ---bfile /opt/galaxy/test-data/tinywga +--bfile /share/shared/galaxy/test-data/tinywga --make-bed ---out /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1 +--out /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1 --set-hh-missing --mind 1 --geno 1 @@ -25,16 +25,16 @@ --hwe 0 --me 1 1 -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 25 SNPs 27 founders and 13 non-founders found @@ -57,10 +57,10 @@ 0 Mendel errors detected in total 0 families ( 0 individuals ) removed due to Mendel errors 0 markers removed due to Mendel errors, 25 remaining -Writing pedigree information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ] -Writing map (extended format) information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ] -Writing genotype bitfile to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ] +Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ] +Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ] +Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ] Using (default) SNP-major mode Converting data to SNP-major format -Analysis finished: Thu Mar 25 21:01:24 2010 +Analysis finished: Sun May 9 21:23:43 2010 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/Rplots.pdf --- a/test-data/rgtestouts/rgEigPCA/Rplots.pdf Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/Rplots.pdf Mon May 10 10:17:11 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210125) -/ModDate (D:20100325210125) +/CreationDate (D:20100509212343) +/ModDate (D:20100509212343) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) @@ -34,10 +34,42 @@ 5 0 obj << /Type /Encoding -/BaseEncoding /WinAnsiEncoding -/Differences [ 45/minus 96/quoteleft -144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent -/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +/BaseEncoding /PDFDocEncoding +/Differences [ + 0/.notdef 1/.notdef 2/.notdef 3/.notdef 4/.notdef 5/.notdef 6/.notdef 7/.notdef + 8/.notdef 9/.notdef 10/.notdef 11/.notdef 12/.notdef 13/.notdef 14/.notdef 15/.notdef + 16/.notdef 17/.notdef 18/.notdef 19/.notdef 20/.notdef 21/.notdef 22/.notdef 23/.notdef + 24/.notdef 25/.notdef 26/.notdef 27/.notdef 28/.notdef 29/.notdef 30/.notdef 31/.notdef + 32/space 33/exclam 34/quotedbl 35/numbersign 36/dollar 37/percent 38/ampersand 39/quoteright + 40/parenleft 41/parenright 42/asterisk 43/plus 44/comma 45/minus 46/period 47/slash + 48/zero 49/one 50/two 51/three 52/four 53/five 54/six 55/seven + 56/eight 57/nine 58/colon 59/semicolon 60/less 61/equal 62/greater 63/question + 64/at 65/A 66/B 67/C 68/D 69/E 70/F 71/G + 72/H 73/I 74/J 75/K 76/L 77/M 78/N 79/O + 80/P 81/Q 82/R 83/S 84/T 85/U 86/V 87/W + 88/X 89/Y 90/Z 91/bracketleft 92/backslash 93/bracketright 94/asciicircum 95/underscore + 96/quoteleft 97/a 98/b 99/c 100/d 101/e 102/f 103/g + 104/h 105/i 106/j 107/k 108/l 109/m 110/n 111/o + 112/p 113/q 114/r 115/s 116/t 117/u 118/v 119/w + 120/x 121/y 122/z 123/braceleft 124/bar 125/braceright 126/asciitilde 127/.notdef + 128/.notdef 129/.notdef 130/.notdef 131/.notdef 132/.notdef 133/.notdef 134/.notdef 135/.notdef + 136/.notdef 137/.notdef 138/.notdef 139/.notdef 140/.notdef 141/.notdef 142/.notdef 143/.notdef + 144/dotlessi 145/grave 146/acute 147/circumflex 148/tilde 149/macron 150/breve 151/dotaccent + 152/dieresis 153/.notdef 154/ring 155/cedilla 156/.notdef 157/hungarumlaut 158/ogonek 159/caron + 160/space 161/exclamdown 162/cent 163/sterling 164/Euro 165/yen 166/Scaron 167/section + 168/scaron 169/copyright 170/ordfeminine 171/guillemotleft 172/logicalnot 173/hyphen 174/registered 175/macron + 176/degree 177/plusminus 178/twosuperior 179/threesuperior 180/Zcaron 181/mu 182/paragraph 183/periodcentered + 184/zcaron 185/onesuperior 186/ordmasculine 187/guillemotright 188/OE 189/oe 190/Ydieresis 191/questiondown + 192/Agrave 193/Aacute 194/Acircumflex 195/Atilde 196/Adieresis 197/Aring 198/AE 199/Ccedilla + 200/Egrave 201/Eacute 202/Ecircumflex 203/Edieresis 204/Igrave 205/Iacute 206/Icircumflex 207/Idieresis + 208/Eth 209/Ntilde 210/Ograve 211/Oacute 212/Ocircumflex 213/Otilde 214/Odieresis 215/multiply + 216/Oslash 217/Ugrave 218/Uacute 219/Ucircumflex 220/Udieresis 221/Yacute 222/Thorn 223/germandbls + 224/agrave 225/aacute 226/acircumflex 227/atilde 228/adieresis 229/aring 230/ae 231/ccedilla + 232/egrave 233/eacute 234/ecircumflex 235/edieresis 236/igrave 237/iacute 238/icircumflex 239/idieresis + 240/eth 241/ntilde 242/ograve 243/oacute 244/ocircumflex 245/otilde 246/odieresis 247/divide + 248/oslash 249/ugrave 250/uacute 251/ucircumflex 252/udieresis 253/yacute 254/thorn 255/ydieresis + +] legend("top",legend=llist,pch=glist,col=glist,title="Sample") grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted") dev.off() -#R script autogenerated by rgenetics/rgutils.py on 25/03/2010 21:01:25 +#R script autogenerated by rgenetics/rgutils.py on 09/05/2010 21:23:43 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html Mon May 10 10:17:11 2010 -0400 @@ -9,30 +9,27 @@ </head> <body> <div class="document"> -<h4>Output from rgEigPCA.py run at 25/03/2010 21:01:25<br/> +<h4>Output from rgEigPCA.py run at 09/05/2010 21:23:43<br/> </h4> -newfilepath=/opt/galaxy/test-data/rgtestouts/rgEigPCA, rexe=R(click on the image below to see a much higher quality PDF version)<table border="0" cellpadding="10" cellspacing="10"><tr><td> +newfilepath=/share/shared/galaxy/test-data/rgtestouts/rgEigPCA, rexe=R(click on the image below to see a much higher quality PDF version)<table border="0" cellpadding="10" cellspacing="10"><tr><td> <a href="rgEigPCAtest1_PCAPlot.pdf"><img src="rgEigPCAtest1_PCAPlot.pdf.png" alt="Samples plotted in first 2 eigenvector space" hspace="10" align="left" /></a></td></tr></table><br/> -<div class="document">All Files:<ol><li><a href="rgEigPCAtest1_eval.xls">rgEigPCAtest1_eval.xls (507 B)</a></li> -<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par (311 B)</a></li> +<div class="document">All Files:<ol><li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li> +<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par (338 B)</a></li> +<li><a href="rgEigPCAtest1.txt">rgEigPCAtest1.txt (3.3 KB)</a></li> +<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt (6.1 KB)</a></li> +<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf (10.4 KB)</a></li> +<li><a href="rgEigPCAtest1_eval.xls">rgEigPCAtest1_eval.xls (507 B)</a></li> +<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls (1.2 KB)</a></li> +<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R (1.6 KB)</a></li> +<li><a href="Rplots.pdf">Rplots.pdf (3.3 KB)</a></li> +<li><a href="rgEigPCAtest1_pca.xls.evec">rgEigPCAtest1_pca.xls.evec (3.3 KB)</a></li> <li><a href="rgEigPCAtest1_PCAPlot.pdf.png">rgEigPCAtest1_PCAPlot.pdf.png (27.1 KB)</a></li> -<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt (6.0 KB)</a></li> -<li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li> -<li><a href="rgEigPCAtest1_eigensoftplot.pdf.xtxt">rgEigPCAtest1_eigensoftplot.pdf.xtxt (257 B)</a></li> -<li><a href="rgEigPCAtest1_eigensoftplot.pdf.ps">rgEigPCAtest1_eigensoftplot.pdf.ps (13.6 KB)</a></li> -<li><a href="rgEigPCAtest1_pca.xls.evec">rgEigPCAtest1_pca.xls.evec (3.3 KB)</a></li> -<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls (1.3 KB)</a></li> -<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf (7.9 KB)</a></li> -<li><a href="rgEigPCAtest1.txt">rgEigPCAtest1.txt (3.3 KB)</a></li> -<li><a href="rgEigPCAtest1_eigensoftplot.pdf.pdf">rgEigPCAtest1_eigensoftplot.pdf.pdf (2.1 KB)</a></li> -<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R (1.6 KB)</a></li> -<li><a href="Rplots.pdf">Rplots.pdf (813 B)</a></li> </ol></div><div class="document">Log rgEigPCAtest1_log.txt contents follow below<p/><pre>parameter file: rgEigPCAtest1_pca.xls.par ### THE INPUT PARAMETERS ##PARAMETER NAME: VALUE -genotypename: /opt/galaxy/test-data/tinywga.ped -snpname: /opt/galaxy/test-data/tinywga.map -indivname: /opt/galaxy/test-data/tinywga.ped +genotypename: /share/shared/galaxy/test-data/tinywga.ped +snpname: /share/shared/galaxy/test-data/tinywga.map +indivname: /share/shared/galaxy/test-data/tinywga.ped evecoutname: rgEigPCAtest1_pca.xls.evec evaloutname: rgEigPCAtest1_eval.xls altnormstyle: NO @@ -156,5 +153,5 @@ Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193 Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069 </pre></div>If you need to rerun this analysis, the command line used was -smartpca.perl -i /opt/galaxy/test-data/tinywga.ped -a /opt/galaxy/test-data/tinywga.map -b /opt/galaxy/test-data/tinywga.ped -o rgEigPCAtest1_pca.xls -p rgEigPCAtest1_eigensoftplot.pdf -e rgEigPCAtest1_eval.xls -l rgEigPCAtest1_log.txt -k 4 -m 2 -t 2 -s 2 +smartpca.perl -i /share/shared/galaxy/test-data/tinywga.ped -a /share/shared/galaxy/test-data/tinywga.map -b /share/shared/galaxy/test-data/tinywga.ped -o rgEigPCAtest1_pca.xls -p rgEigPCAtest1_eigensoftplot.pdf -e rgEigPCAtest1_eval.xls -l rgEigPCAtest1_log.txt -k 4 -m 2 -t 2 -s 2 <p/></div></body></html> diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf Mon May 10 10:17:11 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210125) -/ModDate (D:20100325210125) +/CreationDate (D:20100509212343) +/ModDate (D:20100509212343) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) @@ -410,10 +410,42 @@ 8 0 obj << /Type /Encoding -/BaseEncoding /WinAnsiEncoding -/Differences [ 45/minus 96/quoteleft -144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent -/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +/BaseEncoding /PDFDocEncoding +/Differences [ + 0/.notdef 1/.notdef 2/.notdef 3/.notdef 4/.notdef 5/.notdef 6/.notdef 7/.notdef + 8/.notdef 9/.notdef 10/.notdef 11/.notdef 12/.notdef 13/.notdef 14/.notdef 15/.notdef + 16/.notdef 17/.notdef 18/.notdef 19/.notdef 20/.notdef 21/.notdef 22/.notdef 23/.notdef + 24/.notdef 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139/.notdef 140/.notdef 141/.notdef 142/.notdef 143/.notdef + 144/dotlessi 145/grave 146/acute 147/circumflex 148/tilde 149/macron 150/breve 151/dotaccent + 152/dieresis 153/.notdef 154/ring 155/cedilla 156/.notdef 157/hungarumlaut 158/ogonek 159/caron + 160/space 161/exclamdown 162/cent 163/sterling 164/Euro 165/yen 166/Scaron 167/section + 168/scaron 169/copyright 170/ordfeminine 171/guillemotleft 172/logicalnot 173/hyphen 174/registered 175/macron + 176/degree 177/plusminus 178/twosuperior 179/threesuperior 180/Zcaron 181/mu 182/paragraph 183/periodcentered + 184/zcaron 185/onesuperior 186/ordmasculine 187/guillemotright 188/OE 189/oe 190/Ydieresis 191/questiondown + 192/Agrave 193/Aacute 194/Acircumflex 195/Atilde 196/Adieresis 197/Aring 198/AE 199/Ccedilla + 200/Egrave 201/Eacute 202/Ecircumflex 203/Edieresis 204/Igrave 205/Iacute 206/Icircumflex 207/Idieresis + 208/Eth 209/Ntilde 210/Ograve 211/Oacute 212/Ocircumflex 213/Otilde 214/Odieresis 215/multiply + 216/Oslash 217/Ugrave 218/Uacute 219/Ucircumflex 220/Udieresis 221/Yacute 222/Thorn 223/germandbls + 224/agrave 225/aacute 226/acircumflex 227/atilde 228/adieresis 229/aring 230/ae 231/ccedilla + 232/egrave 233/eacute 234/ecircumflex 235/edieresis 236/igrave 237/iacute 238/icircumflex 239/idieresis + 240/eth 241/ntilde 242/ograve 243/oacute 244/ocircumflex 245/otilde 246/odieresis 247/divide + 248/oslash 249/ugrave 250/uacute 251/ucircumflex 252/udieresis 253/yacute 254/thorn 255/ydieresis + +] trailer << /Size 11 @@ -450,5 +482,5 @@ /Root 2 0 R parameter file: rgEigPCAtest1_pca.xls.par ### THE INPUT PARAMETERS ##PARAMETER NAME: VALUE -genotypename: /opt/galaxy/test-data/tinywga.ped -snpname: /opt/galaxy/test-data/tinywga.map -indivname: /opt/galaxy/test-data/tinywga.ped +genotypename: /share/shared/galaxy/test-data/tinywga.ped +snpname: /share/shared/galaxy/test-data/tinywga.map +indivname: /share/shared/galaxy/test-data/tinywga.ped evecoutname: rgEigPCAtest1_pca.xls.evec evaloutname: rgEigPCAtest1_eval.xls altnormstyle: NO diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls Mon May 10 10:17:11 2010 -0400 @@ -3,43 +3,43 @@ 7.7400 7.2550 4.2710 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.1608 -0.0349 0.0222 0.1244 - -0.1027 0.2939 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2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par Mon May 10 10:17:11 2010 -0400 @@ -1,6 +1,6 @@ -genotypename: /opt/galaxy/test-data/tinywga.ped -snpname: /opt/galaxy/test-data/tinywga.map -indivname: /opt/galaxy/test-data/tinywga.ped +genotypename: /share/shared/galaxy/test-data/tinywga.ped +snpname: /share/shared/galaxy/test-data/tinywga.map +indivname: /share/shared/galaxy/test-data/tinywga.ped evecoutname: rgEigPCAtest1_pca.xls.evec evaloutname: rgEigPCAtest1_eval.xls altnormstyle: NO diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt --- a/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Mon May 10 10:17:11 2010 -0400 @@ -1,13 +1,13 @@ Reading genotypes for 40 subjects and 5 markers Calculating 780 pairs... Estimated time is 0.00 to 0.00 seconds ... -T1: 0.00229454040527 T2: 0.0166795253754 T3: 0.000442743301392 TOT: 0.0201091766357 0 pairs with no (or not enough) comparable genotypes (0.0%) +T1: 0.00482821464539 T2: 0.0623338222504 T3: 0.000771522521973 TOT: 0.0691449642181 0 pairs with no (or not enough) comparable genotypes (0.0%) Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parentchild: mean(mean)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22 +Relstate parentchild: mean(mean)=1.73 sdev(mean)=0.20, mean(sdev)=0.38 sdev(sdev)=0.23 Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parents: mean(mean)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29 -Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 sdev(sdev)=0.22 +Relstate parents: mean(mean)=1.63 sdev(mean)=0.20, mean(sdev)=0.54 sdev(sdev)=0.22 +Relstate unrelated: mean(mean)=1.55 sdev(mean)=0.24, mean(sdev)=0.59 sdev(sdev)=0.24 Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 780 pairs are available of 780 Outliers: 0 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgGRR/rgGRRtest1.html --- a/test-data/rgtestouts/rgGRR/rgGRRtest1.html Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.html Mon May 10 10:17:11 2010 -0400 @@ -9,34 +9,34 @@ </head> <body> <div class="document"> -<h4><div>Output from rgGRR.py run at 15/04/2010 13:12:45<br> +<h4><div>Output from rgGRR.py run at 09/05/2010 21:23:42<br> </h4> If you need to rerun this analysis, the command line was -<pre>'/opt/galaxy/tools/rgenetics/rgGRR.py' '/opt/galaxy/test-data/tinywga' 'tinywga' '/opt/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/opt/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6'</pre> +<pre>'/share/shared/galaxy/tools/rgenetics/rgGRR.py' '/share/shared/galaxy/test-data/tinywga' 'tinywga' '/share/shared/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/share/shared/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6' 'true'</pre> </div> <embed src="rgGRRtest1.svg" type="image/svg+xml" width="1150" height="600" /><div><h4>Click the links below to save output files and plots</h4><br><ol> <li><a href="rgGRRtest1.svg" type="image/svg+xml" >rgGRR Plot (requires SVG)</a></li> <li><a href="rgGRRtest1_table.xls">Mean by SD alleles shared - 780 rows</a></li> +<li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li> <li><a href="rgGRRtest1.html">rgGRRtest1.html</a></li> -<li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li> </ol></div><div><h2>Outliers in tab delimited files linked above are also listed below</h2></div><div><hr><h3>Log from this job (also stored in Log_rgGRRtest1.txt)</h3><pre>Reading genotypes for 40 subjects and 5 markers Calculating 780 pairs... Estimated time is 0.00 to 0.00 seconds ... -T1: 0.00229454040527 T2: 0.0166795253754 T3: 0.000442743301392 TOT: 0.0201091766357 0 pairs with no (or not enough) comparable genotypes (0.0%) +T1: 0.00482821464539 T2: 0.0623338222504 T3: 0.000771522521973 TOT: 0.0691449642181 0 pairs with no (or not enough) comparable genotypes (0.0%) Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parentchild: mean(mean)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22 +Relstate parentchild: mean(mean)=1.73 sdev(mean)=0.20, mean(sdev)=0.38 sdev(sdev)=0.23 Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parents: mean(mean)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29 +Relstate parents: mean(mean)=1.63 sdev(mean)=0.20, mean(sdev)=0.54 sdev(sdev)=0.22 -Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 sdev(sdev)=0.22 +Relstate unrelated: mean(mean)=1.55 sdev(mean)=0.24, mean(sdev)=0.59 sdev(sdev)=0.24 Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgGRR/rgGRRtest1.svg --- a/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Mon May 10 10:17:11 2010 -0400 @@ -252,93 +252,97 @@ <!-- One group/layer of points for each relationship type --> <g id="unrelated" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;" cursor="pointer"> -<circle cx="0" cy="600" r="2" - onmouseover="showBTT(evt, 5, 1.00, 0.00, 0.00, 0.00, 2, 2, 0, 2, 2)" +<circle cx="-287" cy="25" r="2" onmouseover="showOTT(evt, 5, '13,2,0,0', '1344,1,12,13', 0.75, 0.96, 4, 1.55, 0.59)" onmouseout="hideOTT(evt)" /> +<circle cx="575" cy="0" r="2" + onmouseover="showBTT(evt, 5, 1.50, 0.00, 1.00, 0.00, 11, 2, 0, 2, 2)" + onmouseout="hideBTT(evt)" /> +<circle 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1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_14 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_14 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_2 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5 +1341_2 1344_12 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_2 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_2 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5 +1344_1 1344_12 1.400000 0.894427 -0.642422 0.715735 5 5 +1344_1 1344_13 1.400000 0.894427 -0.642422 0.715735 5 5 +1344_1 1345_12 1.400000 0.894427 -2.302185 1.712469 5 5 +1344_12 1344_13 1.400000 0.894427 1.883560 -2.485480 5 5 +1344_12 1345_12 1.400000 0.894427 -0.636142 1.267018 5 5 +1344_13 1345_12 1.400000 0.894427 -0.636142 1.267018 5 5 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG Binary file test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt --- a/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt Mon May 10 10:17:11 2010 -0400 @@ -1,7 +1,7 @@ -PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin +PATH=/share/apps:/share/shared/lx26-amd64/bin:/udd/rerla/bin:/share/shared/lx26-amd64/bin:/opt/gridengine/bin/lx26-amd64:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maven/bin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin:/opt/gridengine:/bin/lx26-amd64:/usr/X11R6/bin ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region -## executing java -jar /opt/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0 +## executing java -jar /share/shared/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0 ## executing mogrify -resize 800x400! *.PNG returned 0 ## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0 ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0 @@ -12,16 +12,16 @@ ## executing pdfjoin "*.pdf" --fitpaper true --outfile alljoin.pdf returned 0 ## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0 ***************************************************** -Haploview 4.2 Java Version: 1.6.0_03 +Haploview 4.2 Java Version: 1.6.0_13 ***************************************************** -Arguments: -n -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 +Arguments: -n -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 Max LD comparison distance = 200000kb -Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info +Using data file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped +Using marker information file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info 10 out of 10 markers passed the MAF threshold. 10 out of 10 markers passed the Mendel threshold. 10 out of 10 markers passed the genotyping threshold. @@ -33,11 +33,11 @@ Writing output to rgHaploViewtest1.ped.TESTS Writing output to rgHaploViewtest1.ped.CHAPS ***************************************************** -Haploview 4.2 Java Version: 1.6.0_03 +Haploview 4.2 Java Version: 1.6.0_13 ***************************************************** -Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng +Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng Max LD comparison distance = 200000kb diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/alljoin.pdf Binary file test-data/rgtestouts/rgHaploView/alljoin.pdf has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/allnup.pdf Binary file test-data/rgtestouts/rgHaploView/allnup.pdf has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html --- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html Mon May 10 10:17:11 2010 -0400 @@ -23,13 +23,13 @@ <li><a href="rgHaploViewtest1.ped.LD.PNG">rgHaploViewtest1.ped.LD.PNG - rgHaploViewtest1.ped.LD.PNG</a></li> <li><a href="rgHaploViewtest1.ped.TAGS">rgHaploViewtest1.ped.TAGS - rgHaploViewtest1.ped.TAGS Tagger output</a></li> <li><a href="rgHaploViewtest1.ped.TESTS">rgHaploViewtest1.ped.TESTS - rgHaploViewtest1.ped.TESTS Tagger output</a></li> -</ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin +</ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>PATH=/share/apps:/share/shared/lx26-amd64/bin:/udd/rerla/bin:/share/shared/lx26-amd64/bin:/opt/gridengine/bin/lx26-amd64:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maven/bin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin:/opt/gridengine:/bin/lx26-amd64:/usr/X11R6/bin ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region -## executing java -jar /opt/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0 +## executing java -jar /share/shared/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0 ## executing mogrify -resize 800x400! *.PNG returned 0 @@ -51,7 +51,7 @@ ***************************************************** -Haploview 4.2 Java Version: 1.6.0_03 +Haploview 4.2 Java Version: 1.6.0_13 ***************************************************** @@ -59,7 +59,7 @@ -Arguments: -n -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 +Arguments: -n -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 @@ -67,9 +67,9 @@ Max LD comparison distance = 200000kb -Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped +Using data file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info +Using marker information file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info 10 out of 10 markers passed the MAF threshold. @@ -93,7 +93,7 @@ ***************************************************** -Haploview 4.2 Java Version: 1.6.0_03 +Haploview 4.2 Java Version: 1.6.0_13 ***************************************************** @@ -101,7 +101,7 @@ -Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng +Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG Binary file test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS --- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS Mon May 10 10:17:11 2010 -0400 @@ -9,17 +9,17 @@ rs3788347 rs3788347 1.0 rs756632 rs756632 1.0 rs4820539 rs4820539 1.0 -rs2283804 rs2267006 1.0 -rs2267006 rs2267006 1.0 +rs2283804 rs2283804 1.0 +rs2267006 rs2283804 1.0 rs4822363 rs4822363 1.0 Test Alleles Captured -rs2267006 rs2267006,rs2283804 -rs4820539 rs4820539 -rs3788347 rs3788347 +rs2283804 rs2267006,rs2283804 rs756632 rs756632 +rs2283802 rs2283802 +rs4820537 rs4820537 rs2267000 rs2267000 rs4822363 rs4822363 -rs2283802 rs2283802 -rs4820537 rs4820537 rs16997606 rs16997606 +rs3788347 rs3788347 +rs4820539 rs4820539 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS --- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS Mon May 10 10:17:11 2010 -0400 @@ -1,9 +1,9 @@ -rs2267006 -rs4820539 -rs3788347 +rs2283804 rs756632 +rs2283802 +rs4820537 rs2267000 rs4822363 -rs2283802 -rs4820537 rs16997606 +rs3788347 +rs4820539 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed Mon May 10 10:17:11 2010 -0400 @@ -1,1 +1,1 @@ -lÿÿÿÿûÿúÿÿÿmÿÿÿýÿÿÿÿÿ:ú¢ÿ¿«¯ü( \ No newline at end of file +lú £ïªîþ¨:*»ïêìª,«Àÿÿÿÿûÿúÿÿÿ \ No newline at end of file diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim Mon May 10 10:17:11 2010 -0400 @@ -1,3 +1,3 @@ +22 rs3788347 0 21797804 3 1 +22 rs5759608 0 21832708 2 4 22 rs2267010 0 21864366 3 1 -22 rs12160770 0 21892925 1 3 -22 rs4822375 0 21905642 1 3 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log Mon May 10 10:17:11 2010 -0400 @@ -1,9 +1,9 @@ -## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 25/03/2010 21:01:24 +## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 09/05/2010 21:23:42 ## Rgenetics January 4 2010: http://rgenetics.org Galaxy Tools rgLDIndep.py Plink pruneLD runner -## ldindep now executing plink --noweb --bfile /opt/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1 +## 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 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -12,30 +12,30 @@ @----------------------------------------------------------@ Skipping web check... [ --noweb ] -Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] -Analysis started: Thu Mar 25 21:01:24 2010 +Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] +Analysis started: Sun May 9 21:23:42 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga + --bfile /share/shared/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 - --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 + --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1 -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 25 SNPs 27 founders and 13 non-founders found @@ -60,20 +60,20 @@ 0 markers removed due to Mendel errors, 25 remaining Converting data to SNP-major format Performing LD-based pruning... -Writing pruned-in SNPs to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] -Writing pruned-out SNPs to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ] +Writing pruned-in SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] +Writing pruned-out SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ] Scanning from chromosome 22 to 22 Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ] For chromosome 22, 22 SNPs pruned out, 3 remaining -Analysis finished: Thu Mar 25 21:01:24 2010 +Analysis finished: Sun May 9 21:23:42 2010 -## ldindep now executing plink --noweb --bfile /opt/galaxy/test-data/tinywga --extract /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 +## 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 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -82,48 +82,48 @@ @----------------------------------------------------------@ Skipping web check... [ --noweb ] -Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] -Analysis started: Thu Mar 25 21:01:24 2010 +Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] +Analysis started: Sun May 9 21:23:42 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga - --extract /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in + --bfile /share/shared/galaxy/test-data/tinywga + --extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed - --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 + --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode -Reading list of SNPs to extract [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read +Reading list of SNPs to extract [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read Before frequency and genotyping pruning, there are 3 SNPs 27 founders and 13 non-founders found -Total genotyping rate in remaining individuals is 0.975 +Total genotyping rate in remaining individuals is 1 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 3 SNPs After filtering, 10 cases, 30 controls and 0 missing After filtering, 21 males, 19 females, and 0 of unspecified sex -Writing pedigree information to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] -Writing map (extended format) information to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] -Writing genotype bitfile to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] +Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] +Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] +Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] Using (default) SNP-major mode -Analysis finished: Thu Mar 25 21:01:24 2010 +Analysis finished: Sun May 9 21:23:42 2010 -## ldindep now executing plink --noweb --bfile /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 +## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -132,38 +132,38 @@ @----------------------------------------------------------@ Skipping web check... [ --noweb ] -Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] -Analysis started: Thu Mar 25 21:01:24 2010 +Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] +Analysis started: Sun May 9 21:23:42 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 + --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode - --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 + --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 -Reading map (extended format) from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] -3 markers to be included from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] -40 individuals read from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] +3 markers to be included from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 3 SNPs 27 founders and 13 non-founders found -Total genotyping rate in remaining individuals is 0.975 +Total genotyping rate in remaining individuals is 1 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 3 SNPs After filtering, 10 cases, 30 controls and 0 missing After filtering, 21 males, 19 females, and 0 of unspecified sex -Writing recoded ped file to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] -Writing new map file to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] +Writing recoded ped file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] +Writing new map file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] -Analysis finished: Thu Mar 25 21:01:24 2010 +Analysis finished: Sun May 9 21:23:42 2010 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map Mon May 10 10:17:11 2010 -0400 @@ -1,3 +1,3 @@ +22 rs3788347 0 21797804 +22 rs5759608 0 21832708 22 rs2267010 0 21864366 -22 rs12160770 0 21892925 -22 rs4822375 0 21905642 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped Mon May 10 10:17:11 2010 -0400 @@ -1,40 +1,40 @@ -101 1 3 2 2 2 1 1 0 0 1 3 -101 2 0 0 2 1 1 1 3 3 1 3 -101 3 0 0 1 1 1 1 1 3 3 3 -105 1 3 2 2 2 1 1 0 0 1 1 -105 2 0 0 2 1 1 1 3 3 1 3 -105 3 0 0 1 1 1 1 3 3 1 3 -112 1 3 2 1 2 1 1 3 3 3 3 -112 2 0 0 2 1 1 1 3 3 3 3 -112 3 0 0 1 1 1 1 3 3 1 3 -117 1 3 2 2 2 1 1 3 3 1 1 -117 2 0 0 2 1 1 1 3 3 1 3 -117 3 0 0 1 1 1 1 3 3 1 3 -12 1 3 2 1 2 1 1 3 3 3 3 -12 2 0 0 2 1 1 1 3 3 3 3 -12 3 0 0 1 1 1 1 3 3 3 3 -13 1 3 2 1 2 1 1 3 3 3 3 -13 2 0 0 2 1 1 1 0 0 3 3 -13 3 0 0 1 1 3 1 3 3 3 3 -1334 1 10 11 1 2 1 1 3 3 3 3 -1334 10 0 0 1 1 1 1 3 3 1 3 -1334 11 0 0 2 1 1 1 3 3 3 3 -1334 12 0 0 1 1 1 1 3 3 1 3 -1334 13 0 0 2 1 1 1 3 3 1 3 -1334 2 12 13 2 2 1 1 3 3 1 3 -1340 1 9 10 1 2 3 1 3 3 3 3 -1340 10 0 0 2 1 3 1 3 3 3 3 -1340 11 0 0 1 1 1 1 3 3 1 3 -1340 12 0 0 2 1 1 1 3 3 1 3 -1340 2 11 12 2 2 1 1 3 3 1 3 -1340 9 0 0 1 1 1 1 3 3 3 3 -1341 1 11 12 1 1 1 1 3 3 1 1 -1341 11 0 0 1 1 1 1 3 3 1 3 -1341 12 0 0 2 1 1 1 3 3 1 1 -1341 13 0 0 1 1 1 1 3 3 3 3 -1341 14 0 0 2 1 1 1 3 3 3 3 -1341 2 13 14 2 1 1 1 3 3 3 3 -1344 1 12 13 1 1 1 1 3 3 1 1 -1344 12 0 0 1 1 1 1 3 3 1 3 -1344 13 0 0 2 1 1 1 3 3 1 3 -1345 12 0 0 1 1 1 1 3 3 1 1 +101 1 3 2 2 2 3 3 2 4 1 1 +101 2 0 0 2 1 3 3 2 4 1 1 +101 3 0 0 1 1 3 3 4 4 1 1 +105 1 3 2 2 2 3 1 2 2 1 1 +105 2 0 0 2 1 3 1 2 4 1 1 +105 3 0 0 1 1 3 1 2 4 1 1 +112 1 3 2 1 2 1 1 2 4 1 1 +112 2 0 0 2 1 1 1 2 2 1 1 +112 3 0 0 1 1 3 1 4 4 1 1 +117 1 3 2 2 2 3 3 2 4 1 1 +117 2 0 0 2 1 3 3 4 4 1 1 +117 3 0 0 1 1 3 3 2 4 1 1 +12 1 3 2 1 2 3 3 4 4 1 1 +12 2 0 0 2 1 3 3 4 4 1 1 +12 3 0 0 1 1 3 1 2 4 1 1 +13 1 3 2 1 2 3 1 4 4 1 1 +13 2 0 0 2 1 1 1 2 4 1 1 +13 3 0 0 1 1 3 3 2 4 3 1 +1334 1 10 11 1 2 3 1 2 4 1 1 +1334 10 0 0 1 1 3 1 4 4 1 1 +1334 11 0 0 2 1 1 1 2 2 1 1 +1334 12 0 0 1 1 1 1 4 4 1 1 +1334 13 0 0 2 1 3 1 2 4 1 1 +1334 2 12 13 2 2 1 1 4 4 1 1 +1340 1 9 10 1 2 3 1 2 4 3 1 +1340 10 0 0 2 1 3 1 2 4 3 1 +1340 11 0 0 1 1 3 1 2 4 1 1 +1340 12 0 0 2 1 3 1 2 4 1 1 +1340 2 11 12 2 2 3 1 2 2 1 1 +1340 9 0 0 1 1 1 1 4 4 1 1 +1341 1 11 12 1 1 3 1 2 4 1 1 +1341 11 0 0 1 1 1 1 2 2 1 1 +1341 12 0 0 2 1 3 1 4 4 1 1 +1341 13 0 0 1 1 1 1 2 4 1 1 +1341 14 0 0 2 1 1 1 2 4 1 1 +1341 2 13 14 2 1 1 1 2 4 1 1 +1344 1 12 13 1 1 3 3 2 2 1 1 +1344 12 0 0 1 1 3 1 2 2 1 1 +1344 13 0 0 2 1 3 1 2 2 1 1 +1345 12 0 0 1 1 3 1 4 4 1 1 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in Mon May 10 10:17:11 2010 -0400 @@ -1,3 +1,3 @@ +rs3788347 +rs5759608 rs2267010 -rs12160770 -rs4822375 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out Mon May 10 10:17:11 2010 -0400 @@ -2,14 +2,12 @@ rs2267000 rs16997606 rs4820537 -rs3788347 rs756632 rs4820539 rs2283804 rs2267006 rs4822363 rs5751592 -rs5759608 rs5759612 rs2267009 rs5759636 @@ -17,6 +15,8 @@ rs2267013 rs6003566 rs2256725 +rs12160770 rs5751611 rs762601 rs2156921 +rs4822375 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Allelep_manhattan.png Binary file test-data/rgtestouts/rgManQQ/Allelep_manhattan.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Allelep_qqplot.png Binary file test-data/rgtestouts/rgManQQ/Allelep_qqplot.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png Binary file test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png Binary file test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/rgManQQtest1.R --- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.R Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.R Mon May 10 10:17:11 2010 -0400 @@ -108,7 +108,7 @@ if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) plot } -rgqqMan = function(infile="/opt/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(6,8), +rgqqMan = function(infile="/share/shared/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(6,8), title="rgManQQtest1",grey=0) { rawd = read.table(infile,head=T,sep=' ')
participants (1)
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Nate Coraor