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Haploview 4.2	Java Version: 1.6.0_03
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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	-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
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
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Haploview 4.2	Java Version: 1.6.0_03
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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
This is pdfjoin version 1.20
Reading site configuration from /etc/pdfnup.conf
  Temporary LaTeX file for this job is /var/tmp/22578.tex
  Calling pdflatex...
  Finished: output is /opt/galaxy/test-data/rgtestouts/rgHaploView/alljoin.pdf
This is pdfnup version 1.20
Reading site configuration from /etc/pdfnup.conf
Processing alljoin.pdf...
  Temporary LaTeX file for this job is /var/tmp/22621-1.tex
  Calling pdflatex...
  Finished: output is /opt/galaxy/test-data/rgtestouts/rgHaploView/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 /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/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