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

https://bitbucket.org/cistrome/cistrome-harvard/ · Plain Text · 58 lines · 49 code · 9 blank · 0 comment · 0 complexity · d8903edfa08125cbb1895bd4730416d7 MD5 · raw file 

    

  1. *****************************************************
    2. 

  2. Haploview 4.2	Java Version: 1.6.0_03
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  3. *****************************************************
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  4. 

  5. 

  6. 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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  7. 

  8. 

  9. Max LD comparison distance = 200000kb
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  10. Using data file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped
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  11. Using marker information file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info
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  12. Writing output to rgHaploViewtest1.ped.LD.PNG
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  13. Starting tagging.
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  14. Writing output to rgHaploViewtest1.ped.TAGS
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  15. Writing output to rgHaploViewtest1.ped.TESTS
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  16. Writing output to rgHaploViewtest1.ped.CHAPS
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  17. release = 21
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  18. *****************************************************
    19. 

  19. Haploview 4.2	Java Version: 1.6.0_03
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  20. *****************************************************
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  21. 

  22. 

  23. Arguments:	-n	-chromosome	22	-panel	YRI	-hapmapDownload	-startpos	21784	-endpos	21905	-ldcolorscheme	RSQ	-maxDistance	200000	-compressedpng	
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  24. 

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  26. Max LD comparison distance = 200000kb
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  27. Downloading chromosome 22, analysis panel YRI, 21784..21905 from HapMap release 21.
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  28. Writing output to Chromosome22YRI.LD.PNG
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  29.           ----
    30. 

  30.   pdfjam: This is pdfjam version 2.06.
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  31.   pdfjam: Reading any site-wide or user-specific defaults...
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  32.           (none found)
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  33.   pdfjam: Effective call for this run of pdfjam:
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  34.           /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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  35.   pdfjam: Calling pdflatex...
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  36.   pdfjam: Finished.  Output was to 'alljoin.pdf'.
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  37.           ----
    38. 

  38.   pdfjam: This is pdfjam version 2.06.
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  39.   pdfjam: Reading any site-wide or user-specific defaults...
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  40.           (none found)
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  41.   pdfjam: Effective call for this run of pdfjam:
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  42.           /usr/local/bin/pdfjam --suffix nup --nup '2x1' --landscape --nup '1x2' --outfile allnup.pdf -- alljoin.pdf - 
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  43.   pdfjam: Calling pdflatex...
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  44.   pdfjam: Finished.  Output was to 'allnup.pdf'.
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  45. PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin
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  46. ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region 
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  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. 

  49. ## executing mogrify -resize 800x400! *.PNG returned 0
    50. 

  50. ## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0
    51. 

  51. ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0
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  52. ## executing convert -resize 800x400! Chromosome22YRI.LD.PNG rgHaploViewtest1.tmp.png returned 0
    53. 

  53. ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'HapMap YRI'" rgHaploViewtest1.tmp.png 2_HapMap_YRI_22.png returned 0
    54. 

  54. ### nimages=2
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  55. ## executing mogrify -format pdf -resize 800x400! *.png returned 0
    56. 

  56. ## executing pdfjoin *.pdf --fitpaper true --outfile alljoin.pdf returned 0
    57. 

  57. ## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0
    58. 

  58. ## executing convert -resize x300 allnup.pdf allnup.png returned 0
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