[2026-07-07 05:05:37] downloading cov 105M
[2026-07-07 05:05:56] downloading cov 106M
[2026-07-07 05:06:17] downloading cov 107M
[2026-07-07 05:06:37] downloading cov 109M
[2026-07-07 05:06:57] downloading cov 239M
[2026-07-07 05:07:17] downloading cov 240M
[2026-07-07 05:07:37] downloading cov 241M
[2026-07-07 05:07:57] downloading cov 242M
[2026-07-07 05:08:17] downloading cov 269M
[2026-07-07 05:08:37] downloading cov 270M
[2026-07-07 05:08:57] downloading cov 271M
[2026-07-07 05:09:19] downloading cov 272M
[2026-07-07 05:09:39] downloading cov 69M
[2026-07-07 05:09:56] downloading cov 70M
[2026-07-07 05:10:13] downloading cov 71M
[2026-07-07 05:10:34] downloading cov 72M
[2026-07-07 05:10:52] downloading cov 78M
[2026-07-07 05:11:07] downloading cov 79M
[2026-07-07 05:11:22] downloading cov 80M
[2026-07-07 05:11:38] downloading cov 81M
[2026-07-07 05:11:53] downloading cov 92M
[2026-07-07 05:12:09] downloading cov 94M
[2026-07-07 05:12:24] downloading cov 95M
[2026-07-07 05:12:38] downloading annotation GFF
[2026-07-07 05:12:43] cov files staged: 24 (expect 24); gff lines: 1171045
[2026-07-07 05:12:43] knitting 26-methylkit-object ...


processing file: _run_26-methylkit-object.Rmd
1/24                    
2/24 [setup]            
3/24                    
4/24 [make-output-dir]  
5/24                    
6/24 [fetch-cov]        
7/24                    
8/24 [install-methylkit]
9/24                    
10/24 [sample-sheet]     
11/24                    
12/24 [cov-file-lists]   
13/24                    
14/24 [read-24]          
15/24                    
16/24 [read-23]          
17/24                    
18/24 [filter-23]        
19/24                    
20/24 [unite-23]         
21/24                    
22/24 [retention-table]  
23/24                    
24/24 [session-info]     
output file: 26-methylkit-object.md

[1] "26-methylkit-object.md"
[2026-07-07 06:07:21]   -> 26-methylkit-object.md done
[2026-07-07 06:07:21] knitting 27-methylation-landscape ...


processing file: _run_27-methylation-landscape.Rmd
1/28                    
2/28 [setup]            
3/28                    
4/28 [make-output-dir]  
5/28                    
6/28 [load-object]      
7/28                    
8/28 [per-sample-global]
9/28                    
10/28 [global-mean-check]
11/28                    
12/28 [stats-plots]      
13/28                    
14/28 [classify-cpgs]    
15/28                    
16/28 [bimodality-plot]  
17/28                    
18/28 [unite-24-for-qc]  
19/28                    
20/28 [correlation]      
21/28                    
22/28 [clustering]       
23/28                    
24/28 [pca]              
25/28                    
26/28 [evaluate-93M]     
27/28                    
28/28 [session-info]     
output file: 27-methylation-landscape.md

[1] "27-methylation-landscape.md"
[2026-07-07 07:04:43]   -> 27-methylation-landscape.md done
[2026-07-07 07:04:43] knitting 28-genomic-feature-distribution ...


processing file: _run_28-genomic-feature-distribution.Rmd
1/20                     
2/20 [setup]             
3/20                     
4/20 [make-output-dir]   
5/20                     
6/20 [fetch-gff]         
7/20                     
8/20 [split-gff]         
9/20                     
10/20 [genome-file]       
11/20                     
12/20 [derived-features]  
13/20                     
14/20 [covered-cpg-bed]   
15/20                     
16/20 [intersect-features]
17/20                     
18/20 [feature-summary]   
19/20                     
20/20 [session-info]      
output file: 28-genomic-feature-distribution.md

[1] "28-genomic-feature-distribution.md"
[2026-07-07 07:14:26]   -> 28-genomic-feature-distribution.md done
[2026-07-07 07:14:26] knitting 29-cpg-oe-mosaic ...


processing file: _run_29-cpg-oe-mosaic.Rmd
1/18                    
2/18 [setup]            
3/18                    
4/18 [make-output-dir]  
5/18                    
6/18 [fetch-gff]        
7/18                    
8/18 [load-genome]      
9/18                    
10/18 [cpg-oe]           
11/18                    
12/18 [oe-distribution]  
13/18                    
14/18 [oe-modes]         
15/18                    
16/18 [oe-vs-methylation]
17/18                    
18/18 [session-info]     
output file: 29-cpg-oe-mosaic.md

[1] "29-cpg-oe-mosaic.md"
[2026-07-07 07:19:39]   -> 29-cpg-oe-mosaic.md done
[2026-07-07 07:19:39] Goal 1 landscape analysis complete.
Outputs:
../output/26-methylkit-object:
cpg_retention_by_threshold.csv
filt_23_10x.rds
filt_23_5x.rds
meth_23_10x.rds
meth_23_5x.rds
myobj_23.rds
myobj_24.rds
sample_metadata.csv

../output/27-methylation-landscape:
bimodality_pooled.png
coverage_stats_histograms.pdf
cpg_class_proportions.csv
meth_24_10x.rds
methylation_stats_histograms.pdf
pca_scores.csv
per_sample_global_methylation.csv
sample_clustering.png
sample_correlation.png
sample_pca.png

../output/28-genomic-feature-distribution:
covered_cpg_10x.bed
covered_cpg_10x.sorted.bed
cpg_in_exon.bed
cpg_in_gene.bed
cpg_in_intergenic.bed
cpg_in_intron.bed
cpg_in_mRNA.bed
cpg_in_promoter_1kb.bed
feature_methylation_barplot.png
feature_methylation_summary.csv
features
genome.txt

../output/29-cpg-oe-mosaic: