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/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt

https://bitbucket.org/cistrome/cistrome-harvard/
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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