/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html
HTML | 143 lines | 77 code | 66 blank | 0 comment | 0 complexity | 894340c498976c9536e6743e0a810c1e MD5 | raw file
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 rgHaploView.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>rgenetics for Galaxy rgHaploView.py, wrapping HaploView</h4><table><tr><td><a href="allnup.pdf"><img src="allnup.png" alt="Main combined LD image" hspace="10" align="middle"></td><td>Click the thumbnail at left to download the main combined LD image <a href=allnup.pdf>allnup.pdf</a></td></tr></table> 13<br><div><hr><ul> 14<li><a href="alljoin.pdf">alljoin.pdf - All pdf plots, each on a separate page</a></li> 15<li><a href="allnup.pdf">allnup.pdf - All pdf plots on a single page</a></li> 16<li><a href="allnup.png">allnup.png - allnup.png</a></li> 17<li><a href="1_rgHaploViewtest1.pdf">1_rgHaploViewtest1.pdf - 1_rgHaploViewtest1.pdf</a></li> 18<li><a href="1_rgHaploViewtest1.png">1_rgHaploViewtest1.png - 1_rgHaploViewtest1.png</a></li> 19<li><a href="2_HapMap_YRI_22.pdf">2_HapMap_YRI_22.pdf - Hapmap data</a></li> 20<li><a href="2_HapMap_YRI_22.png">2_HapMap_YRI_22.png - Hapmap data</a></li> 21<li><a href="Chromosome22YRI.LD.PNG">Chromosome22YRI.LD.PNG - Hapmap data</a></li> 22<li><a href="Log_rgHaploViewtest1.txt">Log_rgHaploViewtest1.txt - Log_rgHaploViewtest1.txt</a></li> 23<li><a href="rgHaploViewtest1.info">rgHaploViewtest1.info - rgHaploViewtest1 map data for Haploview input</a></li> 24<li><a href="rgHaploViewtest1.ped">rgHaploViewtest1.ped - rgHaploViewtest1 genotype data for Haploview input</a></li> 25<li><a href="rgHaploViewtest1.ped.LD.PNG">rgHaploViewtest1.ped.LD.PNG - rgHaploViewtest1.ped.LD.PNG</a></li> 26<li><a href="rgHaploViewtest1.ped.TAGS">rgHaploViewtest1.ped.TAGS - rgHaploViewtest1.ped.TAGS Tagger output</a></li> 27<li><a href="rgHaploViewtest1.ped.TESTS">rgHaploViewtest1.ped.TESTS - rgHaploViewtest1.ped.TESTS Tagger output</a></li> 28</ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>***************************************************** 29 30Haploview 4.2 Java Version: 1.6.0_03 31 32***************************************************** 33 34 35 36 37 38Arguments: -n -pairwiseTagging -pedfile /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 39 40 41 42 43 44Max LD comparison distance = 200000kb 45 46Using data file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped 47 48Using marker information file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info 49 50Writing output to rgHaploViewtest1.ped.LD.PNG 51 52Starting tagging. 53 54Writing output to rgHaploViewtest1.ped.TAGS 55 56Writing output to rgHaploViewtest1.ped.TESTS 57 58Writing output to rgHaploViewtest1.ped.CHAPS 59 60release = 21 61 62***************************************************** 63 64Haploview 4.2 Java Version: 1.6.0_03 65 66***************************************************** 67 68 69 70 71 72Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng 73 74 75 76 77 78Max LD comparison distance = 200000kb 79 80Downloading chromosome 22, analysis panel YRI, 21784..21905 from HapMap release 21. 81 82Writing output to Chromosome22YRI.LD.PNG 83 84 ---- 85 86 pdfjam: This is pdfjam version 2.06. 87 88 pdfjam: Reading any site-wide or user-specific defaults... 89 90 (none found) 91 92 pdfjam: Effective call for this run of pdfjam: 93 94 /usr/local/bin/pdfjam --fitpaper 'true' --rotateoversize 'true' --suffix joined --fitpaper 'true' --outfile alljoin.pdf -- 1_rgHaploViewtest1.pdf - 2_HapMap_YRI_22.pdf - 95 96 pdfjam: Calling pdflatex... 97 98 pdfjam: Finished. Output was to 'alljoin.pdf'. 99 100 ---- 101 102 pdfjam: This is pdfjam version 2.06. 103 104 pdfjam: Reading any site-wide or user-specific defaults... 105 106 (none found) 107 108 pdfjam: Effective call for this run of pdfjam: 109 110 /usr/local/bin/pdfjam --suffix nup --nup '2x1' --landscape --nup '1x2' --outfile allnup.pdf -- alljoin.pdf - 111 112 pdfjam: Calling pdflatex... 113 114 pdfjam: Finished. Output was to 'allnup.pdf'. 115 116PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin 117 118## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region 119 120 121 122## executing java -jar /opt/galaxy/tool-data/shared/jars/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 returned 0 123 124## executing mogrify -resize 800x400! *.PNG returned 0 125 126## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0 127 128## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0 129 130## executing convert -resize 800x400! Chromosome22YRI.LD.PNG rgHaploViewtest1.tmp.png returned 0 131 132## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'HapMap YRI'" rgHaploViewtest1.tmp.png 2_HapMap_YRI_22.png returned 0 133 134### nimages=2 135 136## executing mogrify -format pdf -resize 800x400! *.png returned 0 137 138## executing pdfjoin *.pdf --fitpaper true --outfile alljoin.pdf returned 0 139 140## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0 141 142## executing convert -resize x300 allnup.pdf allnup.png returned 0 143</pre><hr></div></body></html>