2017-12-19 13:34:12 0.6 STATUS STARTED RnBeads Pipeline 2017-12-19 13:34:13 0.6 INFO Analysis Title: RnBeads Analysis 2017-12-19 13:34:13 0.6 INFO Initialized report index and saved to index.html 2017-12-19 13:34:13 0.6 STATUS STARTED Loading Data 2017-12-19 13:34:13 0.6 INFO Number of cores: 2 2017-12-19 13:34:13 0.6 INFO Loading data of type "idat.dir" 2017-12-19 13:34:14 0.6 STATUS STARTED Loading Data from IDAT Files 2017-12-19 13:34:14 0.6 INFO Added column barcode to the provided sample annotation table 2017-12-19 13:34:14 0.6 INFO Detected platform: HumanMethylation450 2017-12-19 13:34:42 0.8 STATUS COMPLETED Loading Data from IDAT Files 2017-12-19 13:35:51 0.7 STATUS Loaded data from C:\RnBeads\data\Ziller2011_PLoSGen_450K\dataset\idat 2017-12-19 13:35:52 0.8 STATUS Predicted gender for the loaded samples 2017-12-19 13:35:54 0.8 STATUS Added data loading section to the report 2017-12-19 13:35:54 0.8 STATUS Loaded 12 samples and 485577 sites 2017-12-19 13:35:54 0.8 INFO Output object is of type RnBeadRawSet 2017-12-19 13:35:54 0.8 STATUS COMPLETED Loading Data 2017-12-19 13:36:00 0.7 WARNING Zip not found on this Windows system, this RnBSet object will not be saved. See the instructions for installing ZIP on Windows in the FAQ section of the RnBeads website. 2017-12-19 13:36:00 0.7 INFO Initialized report index and saved to index.html 2017-12-19 13:36:06 0.7 STATUS STARTED Quality Control 2017-12-19 13:36:06 0.7 INFO Number of cores: 2 2017-12-19 13:36:07 0.7 STATUS STARTED Quality Control Section 2017-12-19 13:36:33 0.8 STATUS Added quality control box plots 2017-12-19 13:38:43 0.8 STATUS Added quality control bar plots 2017-12-19 13:38:46 0.8 STATUS Added negative control boxplots 2017-12-19 13:38:46 0.8 STATUS COMPLETED Quality Control Section 2017-12-19 13:38:46 0.8 STATUS STARTED Visualizing SNP Probe Data 2017-12-19 13:38:46 0.8 STATUS STARTED Mixups Visualization Section 2017-12-19 13:38:54 1.0 STATUS Added SNP Heatmap 2017-12-19 13:38:54 1.0 STATUS Calculated Manhattan distances between samples based on SNP probes 2017-12-19 13:38:55 1.0 STATUS Added SNP-based Distances 2017-12-19 13:38:55 1.0 STATUS COMPLETED Mixups Visualization Section 2017-12-19 13:38:55 1.0 STATUS COMPLETED Visualizing SNP Probe Data 2017-12-19 13:39:00 1.0 STATUS COMPLETED Quality Control 2017-12-19 13:39:00 1.0 INFO Initialized report index and saved to index.html 2017-12-19 13:39:07 0.7 STATUS STARTED Preprocessing 2017-12-19 13:39:07 0.7 INFO Number of cores: 2 2017-12-19 13:39:07 0.7 STATUS STARTED Filtering Procedures I 2017-12-19 13:39:08 0.9 STATUS STARTED Removal of SNP-enriched Sites 2017-12-19 13:39:08 0.9 STATUS Removed 10131 sites using SNP criterion "3" 2017-12-19 13:39:09 0.9 STATUS Saved removed sites to C:\RnBeads\reports\rnbeads_report\preprocessing_data/removed_sites_snp.csv 2017-12-19 13:39:09 0.9 STATUS Added a corresponding section to the report 2017-12-19 13:39:09 0.9 STATUS COMPLETED Removal of SNP-enriched Sites 2017-12-19 13:39:09 1.0 INFO Working with a p-value threshold of 0.05 2017-12-19 13:39:09 0.9 STATUS STARTED Greedycut 2017-12-19 13:39:17 0.9 STATUS Calculated a total of 758 iterations 2017-12-19 13:39:17 0.9 INFO Optimal number of iterations is 758 2017-12-19 13:39:20 1.0 STATUS Created ROC plot 2017-12-19 13:39:24 0.9 STATUS Created line plots for matrix dimensions and other statistics 2017-12-19 13:39:24 0.9 STATUS Saved removed sites to C:\RnBeads\reports\rnbeads_report\preprocessing_data/removed_sites_greedycut.csv 2017-12-19 13:39:24 0.9 STATUS COMPLETED Greedycut 2017-12-19 13:39:38 0.7 STATUS Retained 12 samples and 474689 sites 2017-12-19 13:39:38 0.7 STATUS COMPLETED Filtering Procedures I 2017-12-19 13:39:38 0.7 STATUS STARTED Summary of Filtering Procedures I 2017-12-19 13:39:38 0.7 STATUS Creating summary table of removed sites, samples and unreliable measurements... 2017-12-19 13:39:39 1.0 STATUS Saving table and figures... 2017-12-19 13:39:40 1.0 STATUS Added summary table of removed and retained items 2017-12-19 13:39:40 1.0 INFO Subsampling 110888 sites for plotting density distributions 2017-12-19 13:39:41 0.8 STATUS Constructed sequences of removed and retained methylation values 2017-12-19 13:39:52 0.9 STATUS Added comparison between removed and retained beta values 2017-12-19 13:39:52 0.9 STATUS COMPLETED Summary of Filtering Procedures I 2017-12-19 13:39:52 0.9 STATUS STARTED Manipulating the object 2017-12-19 13:41:23 0.9 STATUS Removed 10888 sites (probes) 2017-12-19 13:41:24 0.9 INFO Retained 474689 sites and 12 samples 2017-12-19 13:41:24 0.9 STATUS COMPLETED Manipulating the object 2017-12-19 13:41:24 0.9 STATUS STARTED Normalization Procedure 2017-12-19 13:47:17 1.0 STATUS Performed normalization with method bmiq 2017-12-19 13:48:10 0.8 STATUS Performed normalization with method "bmiq" 2017-12-19 13:48:24 0.9 STATUS Added comparison between non-normalized and normalized beta values 2017-12-19 13:48:26 1.1 STATUS Added histogram of observed beta shifts (magnitude of correction) 2017-12-19 13:48:27 1.1 STATUS Added 2D histogram of observed beta values and shifts 2017-12-19 13:48:29 1.2 STATUS Added normalization section 2017-12-19 13:48:29 1.2 STATUS COMPLETED Normalization Procedure 2017-12-19 13:48:36 0.8 STATUS STARTED Filtering Procedures II 2017-12-19 13:48:37 1.0 INFO Imputation was skipped, data set may still contain missing methylation values 2017-12-19 13:48:37 1.0 STATUS STARTED Probe Context Removal 2017-12-19 13:48:37 1.0 STATUS Removed 3140 probe(s) having not acceptable context 2017-12-19 13:48:37 1.0 STATUS Saved removed sites to C:\RnBeads\reports\rnbeads_report\preprocessing_data/removed_sites_context.csv 2017-12-19 13:48:37 1.0 STATUS Added a corresponding section to the report 2017-12-19 13:48:37 1.0 STATUS COMPLETED Probe Context Removal 2017-12-19 13:48:37 1.0 STATUS STARTED Removal of Sites on Sex Chromosomes 2017-12-19 13:48:37 1.0 STATUS Removed 11122 site(s) on sex chromosomes 2017-12-19 13:48:38 1.0 STATUS Saved removed sites to C:\RnBeads\reports\rnbeads_report\preprocessing_data/removed_sites_sex.csv 2017-12-19 13:48:38 1.0 STATUS Added a corresponding section to the report 2017-12-19 13:48:38 1.0 STATUS COMPLETED Removal of Sites on Sex Chromosomes 2017-12-19 13:48:38 1.0 STATUS Retained 12 samples and 460427 sites 2017-12-19 13:48:38 1.0 STATUS COMPLETED Filtering Procedures II 2017-12-19 13:48:45 0.8 STATUS STARTED Summary of Filtering Procedures II 2017-12-19 13:48:45 0.8 STATUS Creating summary table of removed sites, samples and unreliable measurements... 2017-12-19 13:48:46 0.9 STATUS Saving table and figures... 2017-12-19 13:48:47 0.9 STATUS Added summary table of removed and retained items 2017-12-19 13:48:47 1.0 INFO Subsampling 114262 sites for plotting density distributions 2017-12-19 13:48:47 1.1 STATUS Constructed sequences of removed and retained methylation values 2017-12-19 13:48:58 0.8 STATUS Added comparison between removed and retained beta values 2017-12-19 13:48:58 0.8 STATUS COMPLETED Summary of Filtering Procedures II 2017-12-19 13:48:58 0.8 STATUS STARTED Manipulating the object 2017-12-19 13:50:26 1.0 STATUS Removed 14262 sites (probes) 2017-12-19 13:50:26 1.0 INFO Retained 460427 sites and 12 samples 2017-12-19 13:50:26 1.0 STATUS COMPLETED Manipulating the object 2017-12-19 13:50:34 0.8 STATUS COMPLETED Preprocessing 2017-12-19 13:50:40 0.7 WARNING Zip not found on this Windows system, this RnBSet object will not be saved. See the instructions for installing ZIP on Windows in the FAQ section of the RnBeads website. 2017-12-19 13:50:40 0.7 INFO Initialized report index and saved to index.html 2017-12-19 13:50:47 0.7 STATUS STARTED Tracks and Tables 2017-12-19 13:50:47 0.7 INFO Number of cores: 2 2017-12-19 13:50:48 0.7 STATUS STARTED Generating Tracks and Tables 2017-12-19 13:50:48 0.7 STATUS STARTED Exporting sites 2017-12-19 13:50:48 0.7 STATUS STARTED Creating BED Files 2017-12-19 13:50:48 0.7 STATUS Converting to GRangesList 2017-12-19 13:50:54 0.9 STATUS Exporting sample hES_HUES13_p47 2017-12-19 13:50:57 0.9 STATUS Exporting sample hiPS_20b_p43 2017-12-19 13:51:01 0.9 STATUS Exporting sample hES_HUES1_p29 2017-12-19 13:51:04 1.0 STATUS Exporting sample hiPS_11c_p23 2017-12-19 13:51:07 0.9 STATUS Exporting sample hES_HUES1_p28 2017-12-19 13:51:09 1.0 STATUS Exporting sample hiPS_20b_p49_TeSR 2017-12-19 13:51:12 1.0 STATUS Exporting sample hiPS_20b_p49_KOSR 2017-12-19 13:51:15 1.1 STATUS Exporting sample hiPS_17b_p35_TeSR 2017-12-19 13:51:18 1.1 STATUS Exporting sample hiPS_27b_p31 2017-12-19 13:51:21 0.9 STATUS Exporting sample hES_HUES64_p19 2017-12-19 13:51:24 1.0 STATUS Exporting sample hiPS_17b_p35_KOSR 2017-12-19 13:51:27 0.9 STATUS Exporting sample hES_H9_p58 2017-12-19 13:51:30 1.0 STATUS COMPLETED Creating BED Files 2017-12-19 13:51:30 1.0 STATUS STARTED Creating Track Hub -- bigBed 2017-12-19 13:51:30 1.0 WARNING Skipped conversion bed -> bigBed for region type sites; could not find the tool bedToBigBed 2017-12-19 13:51:30 1.0 STATUS COMPLETED Creating Track Hub -- bigBed 2017-12-19 13:51:30 1.0 STATUS STARTED Creating UCSC Track Hub -- bigWig 2017-12-19 13:51:30 1.0 WARNING Skipped conversion bedGraph -> bigWig for region type sites; could not find the tool bedGraphToBigWig 2017-12-19 13:51:30 1.0 STATUS COMPLETED Creating UCSC Track Hub -- bigWig 2017-12-19 13:51:30 1.0 STATUS COMPLETED Exporting sites 2017-12-19 13:51:31 1.0 STATUS COMPLETED Generating Tracks and Tables 2017-12-19 13:51:31 1.0 STATUS STARTED Writing export report 2017-12-19 13:51:41 1.1 STATUS COMPLETED Writing export report 2017-12-19 13:51:41 1.1 STATUS COMPLETED Tracks and Tables 2017-12-19 13:51:41 1.1 INFO Initialized report index and saved to index.html 2017-12-19 13:51:48 0.7 STATUS STARTED Exploratory Analysis 2017-12-19 13:51:48 0.7 INFO Number of cores: 2 2017-12-19 13:51:49 0.7 STATUS Designed color mappings for probe type and CGI status 2017-12-19 13:52:02 0.9 STATUS STARTED Dimension Reduction Techniques 2017-12-19 13:52:09 1.0 INFO Mapping 4 traits to point colors and types 2017-12-19 13:58:45 0.8 INFO Principal components that explain at least 95 % of the total variance: 9 2017-12-19 13:58:45 0.8 INFO Saved percentage of total variance to pca_variance_explained_1.csv 2017-12-19 13:58:46 0.8 INFO Principal components that explain at least 95 % of the total variance: 9 2017-12-19 13:58:46 0.8 INFO Saved percentage of total variance to pca_variance_explained_2.csv 2017-12-19 13:58:47 0.8 INFO Principal components that explain at least 95 % of the total variance: 8 2017-12-19 13:58:47 0.8 INFO Saved percentage of total variance to pca_variance_explained_3.csv 2017-12-19 13:58:48 0.8 STATUS Created scatter plots and CDFs summarizing the reduced dimensional representations 2017-12-19 13:58:48 0.8 STATUS COMPLETED Dimension Reduction Techniques 2017-12-19 13:58:49 0.8 STATUS STARTED Tests for Associations 2017-12-19 13:58:49 0.8 INFO Testing the following traits for associations: Sample_Group; Cell_Line; Passage_No; Treatment; CellType; Predicted Male Probability; Predicted Gender 2017-12-19 13:58:49 0.8 STATUS Created 10000 sample permutations 2017-12-19 13:59:15 0.8 STATUS Computed correlations between principal components and traits. 2017-12-19 13:59:16 0.8 STATUS Computed pairwise correlations between traits. 2017-12-19 13:59:16 0.8 STATUS COMPLETED Tests for Associations 2017-12-19 13:59:28 1.0 STATUS STARTED Methylation Value Distributions - Sample Groups 2017-12-19 13:59:46 1.0 STATUS COMPLETED Methylation Value Distributions - Sample Groups 2017-12-19 13:59:46 1.0 STATUS STARTED Methylation Value Distributions - Probe Categories 2017-12-19 14:00:18 0.9 STATUS COMPLETED Methylation Value Distributions - Probe Categories 2017-12-19 14:00:19 0.9 STATUS STARTED Sample Clustering 2017-12-19 14:00:19 0.9 STATUS STARTED Agglomerative Hierarchical Clustering 2017-12-19 14:00:20 0.9 STATUS Performed clustering on sites using correlation as a distance metric 2017-12-19 14:00:20 0.9 STATUS Performed clustering on sites using manhattan as a distance metric 2017-12-19 14:00:21 0.9 STATUS Performed clustering on sites using euclidean as a distance metric 2017-12-19 14:00:21 0.9 STATUS Performed clustering on tiling using correlation as a distance metric 2017-12-19 14:00:21 0.9 STATUS Performed clustering on tiling using manhattan as a distance metric 2017-12-19 14:00:21 0.9 STATUS Performed clustering on tiling using euclidean as a distance metric 2017-12-19 14:00:22 0.9 STATUS Performed clustering on promoters using correlation as a distance metric 2017-12-19 14:00:22 0.9 STATUS Performed clustering on promoters using manhattan as a distance metric 2017-12-19 14:00:22 0.9 STATUS Performed clustering on promoters using euclidean as a distance metric 2017-12-19 14:00:22 0.9 STATUS COMPLETED Agglomerative Hierarchical Clustering 2017-12-19 14:00:23 0.8 STATUS STARTED Clustering Section 2017-12-19 14:00:23 0.8 STATUS STARTED Generating Heatmaps 2017-12-19 14:00:23 0.9 STATUS STARTED Region type: sites 2017-12-19 14:05:53 0.9 STATUS COMPLETED Region type: sites 2017-12-19 14:05:53 0.9 STATUS STARTED Region type: tiling 2017-12-19 14:11:42 0.9 STATUS COMPLETED Region type: tiling 2017-12-19 14:11:42 0.9 STATUS STARTED Region type: promoters 2017-12-19 14:17:37 0.9 STATUS COMPLETED Region type: promoters 2017-12-19 14:17:38 0.9 STATUS Created 432 heatmaps based on the clustering results 2017-12-19 14:17:38 0.9 STATUS COMPLETED Generating Heatmaps 2017-12-19 14:17:38 0.9 STATUS STARTED Adding Color Legends 2017-12-19 14:18:29 0.9 STATUS COMPLETED Adding Color Legends 2017-12-19 14:18:29 0.9 STATUS STARTED Estimating Optimal Numbers of Clusters 2017-12-19 14:18:40 0.9 STATUS Estimated number of clusters based on mean silhouette value 2017-12-19 14:18:40 0.9 STATUS COMPLETED Estimating Optimal Numbers of Clusters 2017-12-19 14:18:40 0.9 STATUS STARTED Overlapping Clusters with Sample Traits 2017-12-19 14:18:40 0.9 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_1.csv 2017-12-19 14:18:40 0.9 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_2.csv 2017-12-19 14:18:40 0.9 STATUS Computed adjusted rand indices and saved to exploratory_analysis_data/adjusted_rand_indices_3.csv 2017-12-19 14:18:50 0.9 STATUS COMPLETED Overlapping Clusters with Sample Traits 2017-12-19 14:18:50 0.9 STATUS COMPLETED Clustering Section 2017-12-19 14:18:50 0.9 STATUS COMPLETED Sample Clustering 2017-12-19 14:18:50 0.9 STATUS COMPLETED Exploratory Analysis 2017-12-19 14:18:50 0.9 INFO Initialized report index and saved to index.html 2017-12-19 14:18:57 0.7 STATUS STARTED Differential Methylation 2017-12-19 14:18:57 0.7 INFO Number of cores: 2 2017-12-19 14:18:57 0.7 STATUS STARTED Analysis 2017-12-19 14:18:57 0.7 INFO Using 0 permutation tests 2017-12-19 14:18:58 0.7 INFO Using columns: Sample_Group,Treatment 2017-12-19 14:18:58 0.7 INFO Using region types: tiling,promoters 2017-12-19 14:19:05 0.7 STATUS STARTED Retrieving comparison info 2017-12-19 14:19:05 0.7 STATUS COMPLETED Retrieving comparison info 2017-12-19 14:19:05 0.7 STATUS STARTED Computing differential methylation tables 2017-12-19 14:19:05 0.7 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2017-12-19 14:19:05 0.7 STATUS STARTED Computing Differential Methylation Table 2017-12-19 14:19:05 0.8 INFO Conducting differential analysis using limma 2017-12-19 14:19:45 1.0 STATUS COMPLETED Computing Differential Methylation Table 2017-12-19 14:19:52 0.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2017-12-19 14:23:10 1.0 STATUS Computed table for tiling 2017-12-19 14:24:07 1.2 STATUS Computed table for promoters 2017-12-19 14:24:07 1.2 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2017-12-19 14:24:08 1.2 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2017-12-19 14:24:08 1.2 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2017-12-19 14:24:08 1.2 STATUS STARTED Computing Differential Methylation Table 2017-12-19 14:24:09 1.1 INFO Conducting differential analysis using limma 2017-12-19 14:24:59 1.1 STATUS COMPLETED Computing Differential Methylation Table 2017-12-19 14:25:08 0.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2017-12-19 14:29:02 1.3 STATUS Computed table for tiling 2017-12-19 14:30:00 1.5 STATUS Computed table for promoters 2017-12-19 14:30:00 1.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2017-12-19 14:30:00 1.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2017-12-19 14:30:00 1.4 STATUS COMPLETED Computing differential methylation tables 2017-12-19 14:30:09 0.7 INFO Skipping enrichment analysis of differentially methylated regions 2017-12-19 14:30:09 0.7 STATUS COMPLETED Analysis 2017-12-19 14:30:09 0.7 STATUS STARTED Saving temp objects for debugging 2017-12-19 14:30:09 0.7 WARNING Zip not found on this Windows system, this RnBDiffMeth object will not be saved. See the instructions for installing ZIP on Windows in the FAQ section of the RnBeads website. 2017-12-19 14:30:09 0.7 STATUS COMPLETED Saving temp objects for debugging 2017-12-19 14:30:09 0.7 STATUS STARTED Report Generation 2017-12-19 14:30:09 0.7 STATUS Added introductory section 2017-12-19 14:30:09 0.7 STATUS STARTED Adding Site Level Information 2017-12-19 14:30:09 0.7 STATUS STARTED Selection of rank cutoffs 2017-12-19 14:30:10 1.1 STATUS COMPLETED Selection of rank cutoffs 2017-12-19 14:30:10 1.1 STATUS STARTED Adding scatterplots 2017-12-19 14:38:21 0.7 STATUS COMPLETED Adding scatterplots 2017-12-19 14:38:24 0.7 STATUS STARTED Adding volcano plots 2017-12-19 14:41:51 0.7 STATUS COMPLETED Adding volcano plots 2017-12-19 14:41:52 0.7 STATUS STARTED Adding tables 2017-12-19 14:43:16 1.0 STATUS COMPLETED Adding tables 2017-12-19 14:43:16 1.0 STATUS COMPLETED Adding Site Level Information 2017-12-19 14:43:16 1.0 STATUS STARTED Adding Region Level Information 2017-12-19 14:43:16 1.0 STATUS STARTED Selection of rank cutoffs 2017-12-19 14:43:17 0.9 STATUS COMPLETED Selection of rank cutoffs 2017-12-19 14:43:17 0.9 STATUS STARTED Adding scatterplots 2017-12-19 14:45:28 0.7 STATUS COMPLETED Adding scatterplots 2017-12-19 14:45:29 0.7 STATUS STARTED Adding volcano plots 2017-12-19 15:46:46 0.7 STATUS COMPLETED Adding volcano plots 2017-12-19 15:46:46 0.7 STATUS STARTED Adding tables 2017-12-19 15:47:04 1.0 STATUS COMPLETED Adding tables 2017-12-19 15:47:04 1.0 STATUS COMPLETED Adding Region Level Information 2017-12-19 15:47:04 1.0 STATUS COMPLETED Report Generation 2017-12-19 15:47:05 1.0 STATUS COMPLETED Differential Methylation 2017-12-19 15:47:05 1.0 INFO Initialized report index and saved to index.html 2017-12-19 14:47:17 0.7 STATUS STARTED Saving RData 2017-12-19 14:47:17 0.7 WARNING Zip not found on this Windows system, this RnBDiffMeth object will not be saved. See the instructions for installing ZIP on Windows in the FAQ section of the RnBeads website. 2017-12-19 14:47:18 0.7 STATUS COMPLETED Saving RData 2017-12-19 14:47:27 0.7 STATUS COMPLETED RnBeads Pipeline