processing file: 13.4-wgbs-methylation.Rmd
1/36                  
2/36 [setup]          
3/36                  
4/36 [packages]       
5/36                  
6/36 [parameters]     
7/36                  
8/36 [samples]        
9/36                  
10/36 [align-qc]       
11/36                  
12/36 [read]           
13/36                  
14/36 [snp-mask]       
15/36                  
16/36 [coverage-stats] 
17/36                  
18/36 [filter-unite]   
19/36                  
20/36 [distribution]   
21/36                  
22/36 [pca]            
23/36                  
24/36 [features]       
25/36                  
26/36 [contrasts]      
27/36                  
28/36 [dml]            
29/36                  
30/36 [dmr]            
31/36                  
32/36 [gene-body]      
33/36                  
34/36 [gene-body-limma]
35/36                  
36/36 [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/.claude/worktrees/dna-methylation-ostrea-comparison-4a62b9/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/Rtmpi2A98X/rmarkdown-str1a75215c888df9.html 
[WARNING] Deprecated: --no-highlight. Use --syntax-highlighting=none instead.

Output created: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/.claude/worktrees/dna-methylation-ostrea-comparison-4a62b9/output/13-wgbs/13.4-methylation/13.4-wgbs-methylation.html