/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html
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- <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>
- <br><div><hr><ul>
- <li><a href="alljoin.pdf">alljoin.pdf - All pdf plots, each on a separate page</a></li>
- <li><a href="allnup.pdf">allnup.pdf - All pdf plots on a single page</a></li>
- <li><a href="allnup.png">allnup.png - allnup.png</a></li>
- <li><a href="1_rgHaploViewtest1.pdf">1_rgHaploViewtest1.pdf - 1_rgHaploViewtest1.pdf</a></li>
- <li><a href="1_rgHaploViewtest1.png">1_rgHaploViewtest1.png - 1_rgHaploViewtest1.png</a></li>
- <li><a href="2_HapMap_YRI_22.pdf">2_HapMap_YRI_22.pdf - Hapmap data</a></li>
- <li><a href="2_HapMap_YRI_22.png">2_HapMap_YRI_22.png - Hapmap data</a></li>
- <li><a href="Chromosome22YRI.LD.PNG">Chromosome22YRI.LD.PNG - Hapmap data</a></li>
- <li><a href="Log_rgHaploViewtest1.txt">Log_rgHaploViewtest1.txt - Log_rgHaploViewtest1.txt</a></li>
- <li><a href="rgHaploViewtest1.info">rgHaploViewtest1.info - rgHaploViewtest1 map data for Haploview input</a></li>
- <li><a href="rgHaploViewtest1.ped">rgHaploViewtest1.ped - rgHaploViewtest1 genotype data for Haploview input</a></li>
- <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>*****************************************************
- Haploview 4.2 Java Version: 1.6.0_03
- *****************************************************
- 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
- Max LD comparison distance = 200000kb
- Using data file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
- Using marker information file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
- Writing output to rgHaploViewtest1.ped.LD.PNG
- Starting tagging.
- Writing output to rgHaploViewtest1.ped.TAGS
- Writing output to rgHaploViewtest1.ped.TESTS
- Writing output to rgHaploViewtest1.ped.CHAPS
- release = 21
- *****************************************************
- Haploview 4.2 Java Version: 1.6.0_03
- *****************************************************
- Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng
- Max LD comparison distance = 200000kb
- Downloading chromosome 22, analysis panel YRI, 21784..21905 from HapMap release 21.
- Writing output to Chromosome22YRI.LD.PNG
- ----
- pdfjam: This is pdfjam version 2.06.
- pdfjam: Reading any site-wide or user-specific defaults...
- (none found)
- pdfjam: Effective call for this run of pdfjam:
- /usr/local/bin/pdfjam --fitpaper 'true' --rotateoversize 'true' --suffix joined --fitpaper 'true' --outfile alljoin.pdf -- 1_rgHaploViewtest1.pdf - 2_HapMap_YRI_22.pdf -
- pdfjam: Calling pdflatex...
- pdfjam: Finished. Output was to 'alljoin.pdf'.
- ----
- pdfjam: This is pdfjam version 2.06.
- pdfjam: Reading any site-wide or user-specific defaults...
- (none found)
- pdfjam: Effective call for this run of pdfjam:
- /usr/local/bin/pdfjam --suffix nup --nup '2x1' --landscape --nup '1x2' --outfile allnup.pdf -- alljoin.pdf -
- pdfjam: Calling pdflatex...
- pdfjam: Finished. Output was to 'allnup.pdf'.
- PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/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/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
- ## 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
- ## executing convert -resize 800x400! Chromosome22YRI.LD.PNG rgHaploViewtest1.tmp.png returned 0
- ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'HapMap YRI'" rgHaploViewtest1.tmp.png 2_HapMap_YRI_22.png returned 0
- ### nimages=2
- ## executing mogrify -format pdf -resize 800x400! *.png returned 0
- ## executing pdfjoin *.pdf --fitpaper true --outfile alljoin.pdf returned 0
- ## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0
- ## executing convert -resize x300 allnup.pdf allnup.png returned 0
- </pre><hr></div></body></html>