/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt
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1***************************************************** 2Haploview 4.2 Java Version: 1.6.0_03 3***************************************************** 4 5 6Arguments: -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 7 8 9Max LD comparison distance = 200000kb 10Using data file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped 11Using marker information file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info 12Writing output to rgHaploViewtest1.ped.LD.PNG 13Starting tagging. 14Writing output to rgHaploViewtest1.ped.TAGS 15Writing output to rgHaploViewtest1.ped.TESTS 16Writing output to rgHaploViewtest1.ped.CHAPS 17release = 21 18***************************************************** 19Haploview 4.2 Java Version: 1.6.0_03 20***************************************************** 21 22 23Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng 24 25 26Max LD comparison distance = 200000kb 27Downloading chromosome 22, analysis panel YRI, 21784..21905 from HapMap release 21. 28Writing output to Chromosome22YRI.LD.PNG 29 ---- 30 pdfjam: This is pdfjam version 2.06. 31 pdfjam: Reading any site-wide or user-specific defaults... 32 (none found) 33 pdfjam: Effective call for this run of pdfjam: 34 /usr/local/bin/pdfjam --fitpaper 'true' --rotateoversize 'true' --suffix joined --fitpaper 'true' --outfile alljoin.pdf -- 1_rgHaploViewtest1.pdf - 2_HapMap_YRI_22.pdf - 35 pdfjam: Calling pdflatex... 36 pdfjam: Finished. Output was to 'alljoin.pdf'. 37 ---- 38 pdfjam: This is pdfjam version 2.06. 39 pdfjam: Reading any site-wide or user-specific defaults... 40 (none found) 41 pdfjam: Effective call for this run of pdfjam: 42 /usr/local/bin/pdfjam --suffix nup --nup '2x1' --landscape --nup '1x2' --outfile allnup.pdf -- alljoin.pdf - 43 pdfjam: Calling pdflatex... 44 pdfjam: Finished. Output was to 'allnup.pdf'. 45PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin 46## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region 47 48## 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 49## executing mogrify -resize 800x400! *.PNG returned 0 50## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0 51## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0 52## executing convert -resize 800x400! Chromosome22YRI.LD.PNG rgHaploViewtest1.tmp.png returned 0 53## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'HapMap YRI'" rgHaploViewtest1.tmp.png 2_HapMap_YRI_22.png returned 0 54### nimages=2 55## executing mogrify -format pdf -resize 800x400! *.png returned 0 56## executing pdfjoin *.pdf --fitpaper true --outfile alljoin.pdf returned 0 57## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0 58## executing convert -resize x300 allnup.pdf allnup.png returned 0