[WARNING] Deprecated: --no-highlight. Use --syntax-highlighting=none instead.


processing file: 13.6-wgbs-methylation-landscape.Rmd
1/58                      
2/58 [setup]              
3/58                      
4/58 [packages]           
5/58                      
6/58 [parameters]         
7/58                      
8/58 [samples]            
9/58                      
10/58 [genome]             
11/58                      
12/58 [feature-composition]
13/58                      
14/58 [read]               
15/58                      
16/58 [pooled-filter]      
17/58                      
18/58 [global-per-oyster]  
19/58                      
20/58 [global-distribution]
21/58                      
22/58 [feature-summary]    
23/58                      
24/58 [feature-plots]      
25/58                      
26/58 [feature-enrichment] 
27/58                      
28/58 [feature-per-oyster] 
29/58                      
30/58 [repeats]            
31/58                      
32/58 [windows]            
33/58                      
34/58 [gene-level]         
35/58                      
36/58 [gene-distribution]  
37/58                      
38/58 [gene-structure]     
39/58                      
40/58 [metagene]           
41/58                      
42/58 [exon-rank]          
43/58                      
44/58 [gene-variability]   
45/58                      
46/58 [load-annotation]    
47/58                      
48/58 [annotation-status]  
49/58                      
50/58 [go-tests]           
51/58                      
52/58 [go-plot]            
53/58                      
54/58 [functional-groups]  
55/58                      
56/58 [summary]            
57/58                      
58/58 [session]            
output file: /mmfs1/gscratch/scrubbed/sr320/claude-136hapa-tmp/13.6-wgbs-methylation-landscape.knit.md

/usr/bin/pandoc +RTS -K512m -RTS /mmfs1/gscratch/scrubbed/sr320/claude-136hapa-tmp/13.6-wgbs-methylation-landscape.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-hapa/13.6-landscape/13.6-wgbs-methylation-landscape.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/Rtmp8MyIng/rmarkdown-str11fe2738ee52d6.html 
[WARNING] Deprecated: --no-highlight. Use --syntax-highlighting=none instead.

Output created: output/13-wgbs-hapa/13.6-landscape/13.6-wgbs-methylation-landscape.html