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

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  6. <meta name="generator" content="Galaxy rgHaploView.py tool output - see http://g2.trac.bx.psu.edu/" />
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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>
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  13. <br><div><hr><ul>
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  14. <li><a href="alljoin.pdf">alljoin.pdf - All pdf plots, each on a separate page</a></li>
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  15. <li><a href="allnup.pdf">allnup.pdf - All pdf plots on a single page</a></li>
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  16. <li><a href="allnup.png">allnup.png - allnup.png</a></li>
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  17. <li><a href="1_rgHaploViewtest1.pdf">1_rgHaploViewtest1.pdf - 1_rgHaploViewtest1.pdf</a></li>
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  18. <li><a href="1_rgHaploViewtest1.png">1_rgHaploViewtest1.png - 1_rgHaploViewtest1.png</a></li>
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  19. <li><a href="2_HapMap_YRI_22.pdf">2_HapMap_YRI_22.pdf - Hapmap data</a></li>
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  20. <li><a href="2_HapMap_YRI_22.png">2_HapMap_YRI_22.png - Hapmap data</a></li>
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  21. <li><a href="Chromosome22YRI.LD.PNG">Chromosome22YRI.LD.PNG - Hapmap data</a></li>
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  22. <li><a href="Log_rgHaploViewtest1.txt">Log_rgHaploViewtest1.txt - Log_rgHaploViewtest1.txt</a></li>
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  23. <li><a href="rgHaploViewtest1.info">rgHaploViewtest1.info - rgHaploViewtest1 map data for Haploview input</a></li>
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  24. <li><a href="rgHaploViewtest1.ped">rgHaploViewtest1.ped - rgHaploViewtest1 genotype data for Haploview input</a></li>
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  25. <li><a href="rgHaploViewtest1.ped.LD.PNG">rgHaploViewtest1.ped.LD.PNG - rgHaploViewtest1.ped.LD.PNG</a></li>
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  26. <li><a href="rgHaploViewtest1.ped.TAGS">rgHaploViewtest1.ped.TAGS - rgHaploViewtest1.ped.TAGS Tagger output</a></li>
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  27. <li><a href="rgHaploViewtest1.ped.TESTS">rgHaploViewtest1.ped.TESTS - rgHaploViewtest1.ped.TESTS Tagger output</a></li>
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  28. </ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>*****************************************************
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  30. Haploview 4.2	Java Version: 1.6.0_03
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  32. *****************************************************
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  38. 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	
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  44. Max LD comparison distance = 200000kb
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  46. Using data file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
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  48. Using marker information file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
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  50. Writing output to rgHaploViewtest1.ped.LD.PNG
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  52. Starting tagging.
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  54. Writing output to rgHaploViewtest1.ped.TAGS
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  56. Writing output to rgHaploViewtest1.ped.TESTS
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  58. Writing output to rgHaploViewtest1.ped.CHAPS
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  59. 

  60. release = 21
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  62. *****************************************************
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  63. 

  64. Haploview 4.2	Java Version: 1.6.0_03
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  66. *****************************************************
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  72. Arguments:	-n	-chromosome	22	-panel	YRI	-hapmapDownload	-startpos	21784	-endpos	21905	-ldcolorscheme	RSQ	-maxDistance	200000	-compressedpng	
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  78. Max LD comparison distance = 200000kb
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  80. Downloading chromosome 22, analysis panel YRI, 21784..21905 from HapMap release 21.
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  82. Writing output to Chromosome22YRI.LD.PNG
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  84.           ----
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  86.   pdfjam: This is pdfjam version 2.06.
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  88.   pdfjam: Reading any site-wide or user-specific defaults...
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  90.           (none found)
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  92.   pdfjam: Effective call for this run of pdfjam:
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  94.           /usr/local/bin/pdfjam --fitpaper 'true' --rotateoversize 'true' --suffix joined --fitpaper 'true' --outfile alljoin.pdf -- 1_rgHaploViewtest1.pdf - 2_HapMap_YRI_22.pdf - 
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  96.   pdfjam: Calling pdflatex...
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  98.   pdfjam: Finished.  Output was to 'alljoin.pdf'.
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  100.           ----
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  102.   pdfjam: This is pdfjam version 2.06.
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  104.   pdfjam: Reading any site-wide or user-specific defaults...
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  106.           (none found)
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  108.   pdfjam: Effective call for this run of pdfjam:
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  110.           /usr/local/bin/pdfjam --suffix nup --nup '2x1' --landscape --nup '1x2' --outfile allnup.pdf -- alljoin.pdf - 
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  112.   pdfjam: Calling pdflatex...
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  114.   pdfjam: Finished.  Output was to 'allnup.pdf'.
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  116. PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin
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  117. 

  118. ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region 
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  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
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  124. ## executing mogrify -resize 800x400! *.PNG returned 0
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  126. ## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0
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  127. 

  128. ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0
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  129. 

  130. ## executing convert -resize 800x400! Chromosome22YRI.LD.PNG rgHaploViewtest1.tmp.png returned 0
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  132. ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'HapMap YRI'" rgHaploViewtest1.tmp.png 2_HapMap_YRI_22.png returned 0
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  133. 

  134. ### nimages=2
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  136. ## executing mogrify -format pdf -resize 800x400! *.png returned 0
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  138. ## executing pdfjoin *.pdf --fitpaper true --outfile alljoin.pdf returned 0
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  139. 

  140. ## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0
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  141. 

  142. ## executing convert -resize x300 allnup.pdf allnup.png returned 0
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  143. </pre><hr></div></body></html>
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