processing file: 13.4-wgbs-methylation.Rmd
1/34                  
2/34 [setup]          
3/34                  
4/34 [packages]       
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6/34 [parameters]     
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8/34 [samples]        
9/34                  
10/34 [align-qc]       
11/34                  
12/34 [read]           
13/34                  
14/34 [coverage-stats] 
15/34                  
16/34 [filter-unite]   
17/34                  
18/34 [distribution]   
19/34                  
20/34 [pca]            
21/34                  
22/34 [features]       
23/34                  
24/34 [contrasts]      
25/34                  
26/34 [dml]            
27/34                  
28/34 [dmr]            
29/34                  
30/34 [gene-body]      
31/34                  
32/34 [gene-body-limma]
33/34                  
34/34 [session]        
output file: 13.4-wgbs-methylation.knit.md

/usr/bin/pandoc +RTS -K512m -RTS 13.4-wgbs-methylation.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/13.4-methylation/13.4-wgbs-methylation.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp8I4t6M/rmarkdown-str9349a3ad01abf.html 
[WARNING] Deprecated: --no-highlight. Use --syntax-highlighting=none instead.

Output created: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/13.4-methylation/13.4-wgbs-methylation.html