/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html

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  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. Haploview 4.2 Java Version: 1.6.0_03
  30. *****************************************************
  31. Arguments: -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
  32. Max LD comparison distance = 200000kb
  33. Using data file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
  34. Using marker information file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
  35. Writing output to rgHaploViewtest1.ped.LD.PNG
  36. Starting tagging.
  37. Writing output to rgHaploViewtest1.ped.TAGS
  38. Writing output to rgHaploViewtest1.ped.TESTS
  39. Writing output to rgHaploViewtest1.ped.CHAPS
  40. release = 21
  41. *****************************************************
  42. Haploview 4.2 Java Version: 1.6.0_03
  43. *****************************************************
  44. Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng
  45. Max LD comparison distance = 200000kb
  46. Downloading chromosome 22, analysis panel YRI, 21784..21905 from HapMap release 21.
  47. Writing output to Chromosome22YRI.LD.PNG
  48. ----
  49. pdfjam: This is pdfjam version 2.06.
  50. pdfjam: Reading any site-wide or user-specific defaults...
  51. (none found)
  52. pdfjam: Effective call for this run of pdfjam:
  53. /usr/local/bin/pdfjam --fitpaper 'true' --rotateoversize 'true' --suffix joined --fitpaper 'true' --outfile alljoin.pdf -- 1_rgHaploViewtest1.pdf - 2_HapMap_YRI_22.pdf -
  54. pdfjam: Calling pdflatex...
  55. pdfjam: Finished. Output was to 'alljoin.pdf'.
  56. ----
  57. pdfjam: This is pdfjam version 2.06.
  58. pdfjam: Reading any site-wide or user-specific defaults...
  59. (none found)
  60. pdfjam: Effective call for this run of pdfjam:
  61. /usr/local/bin/pdfjam --suffix nup --nup '2x1' --landscape --nup '1x2' --outfile allnup.pdf -- alljoin.pdf -
  62. pdfjam: Calling pdflatex...
  63. pdfjam: Finished. Output was to 'allnup.pdf'.
  64. PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin
  65. ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region
  66. ## 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
  67. ## executing mogrify -resize 800x400! *.PNG returned 0
  68. ## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0
  69. ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0
  70. ## executing convert -resize 800x400! Chromosome22YRI.LD.PNG rgHaploViewtest1.tmp.png returned 0
  71. ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'HapMap YRI'" rgHaploViewtest1.tmp.png 2_HapMap_YRI_22.png returned 0
  72. ### nimages=2
  73. ## executing mogrify -format pdf -resize 800x400! *.png returned 0
  74. ## executing pdfjoin *.pdf --fitpaper true --outfile alljoin.pdf returned 0
  75. ## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0
  76. ## executing convert -resize x300 allnup.pdf allnup.png returned 0
  77. </pre><hr></div></body></html>