2013-07-04 12:48:18   STATUS STARTED RnBeads Pipeline
2013-07-04 12:48:18     INFO     Initialized report index and saved to index.html
2013-07-04 12:48:18   STATUS     STARTED Loading Data
2013-07-04 12:48:18   STATUS         STARTED Loading GEO Data Series
2013-07-04 12:53:38     INFO             Loaded 1 data series from GSE38268
2013-07-04 12:53:38     INFO             Extracted 6 samples from series 1
2013-07-04 12:53:38     INFO             Parsed characteristics_ch1 sample information
2013-07-04 12:53:38   STATUS         COMPLETED Loading GEO Data Series
2013-07-04 12:54:49   STATUS         Loaded data from GSE38268. Output object is of class RnBeadSet
2013-07-04 12:54:50   STATUS         Added data loading section
2013-07-04 12:54:50   STATUS     COMPLETED Loading Data
2013-07-04 12:54:50   STATUS     STARTED Normalization
2013-07-04 12:54:50  WARNING         Incompatible values for object and method. Changed the normalization method to "none"
2013-07-04 12:54:50  WARNING         Incompatible values for object and background correction flag. Disabled the background correction
2013-07-04 12:54:50   STATUS         Performed normalization with method "swan"
2013-07-04 12:54:53   STATUS         Added normalization section
2013-07-04 12:54:53   STATUS     COMPLETED Normalization
2013-07-04 12:54:54     INFO     Initialized report index and saved to index.html
2013-07-04 12:54:54   STATUS     STARTED Quality Control
2013-07-04 12:54:54   STATUS         STARTED Quality Control Section
2013-07-04 12:54:54     INFO             No quality information present in the dataset
2013-07-04 12:54:54   STATUS         COMPLETED Quality Control Section
2013-07-04 12:54:54   STATUS     COMPLETED Quality Control
2013-07-04 12:54:54   STATUS     STARTED Visualizing Sample Mixups
2013-07-04 12:54:54   STATUS         STARTED Mixups Visualization Section
2013-07-04 12:55:15   STATUS             Added SNP heatmap
2013-07-04 12:55:15   STATUS         COMPLETED Mixups Visualization Section
2013-07-04 12:55:15   STATUS     COMPLETED Visualizing Sample Mixups
2013-07-04 12:55:15     INFO     Initialized report index and saved to index.html
2013-07-04 12:55:15   STATUS     STARTED Filtering
2013-07-04 12:55:23   STATUS         STARTED Probe Context Removal
2013-07-04 12:56:00   STATUS             Removed 3156 probe(s) out of context
2013-07-04 12:56:01   STATUS             Saved removed sites to /mnt/galaxy/files/000/dataset_3_files/filtering_data/removed_sites_context.csv
2013-07-04 12:56:01   STATUS             Added a corresponding section to the report
2013-07-04 12:56:01   STATUS         COMPLETED Probe Context Removal
2013-07-04 12:56:03   STATUS         STARTED Removal of SNP-enriched Sites
2013-07-04 12:56:38   STATUS             Removed 18987 sites that overlap sites with more than 2 SNP(s)
2013-07-04 12:56:38   STATUS             Saved removed sites to /mnt/galaxy/files/000/dataset_3_files/filtering_data/removed_sites_snp.csv
2013-07-04 12:56:38   STATUS             Added a corresponding section to the report
2013-07-04 12:56:38   STATUS         COMPLETED Removal of SNP-enriched Sites
2013-07-04 12:56:39     INFO         Omitting Greedycut because detection p-values are missing
2013-07-04 12:56:42   STATUS         STARTED Summary of Filtering Procedures
2013-07-04 12:56:46   STATUS             Added summary table of removed and retained values
2013-07-04 12:57:47   STATUS             Added comparison between removed and retained beta values
2013-07-04 12:57:47   STATUS         COMPLETED Summary of Filtering Procedures
2013-07-04 12:57:47   STATUS     COMPLETED Filtering
2013-07-04 12:57:47     INFO     Initialized report index and saved to index.html
2013-07-04 12:57:47   STATUS     STARTED Dimension Reduction Techniques
2013-07-04 12:57:48  WARNING         Removed 4301 loci ( sites ) because they contain missing values
2013-07-04 12:57:49   STATUS         Calculated PCA coordinates
2013-07-04 12:57:49   STATUS         Calculated MDS coordinates using manhattan distance
2013-07-04 12:57:49   STATUS         Calculated MDS coordinates using euclidean distance
2013-07-04 12:57:50  WARNING         Removed 491 loci ( tiling ) because they contain missing values
2013-07-04 12:57:50   STATUS         Calculated PCA coordinates
2013-07-04 12:57:50   STATUS         Calculated MDS coordinates using manhattan distance
2013-07-04 12:57:50   STATUS         Calculated MDS coordinates using euclidean distance
2013-07-04 12:57:50  WARNING         Removed 25 loci ( genes ) because they contain missing values
2013-07-04 12:57:50   STATUS         Calculated PCA coordinates
2013-07-04 12:57:50   STATUS         Calculated MDS coordinates using manhattan distance
2013-07-04 12:57:50   STATUS         Calculated MDS coordinates using euclidean distance
2013-07-04 12:57:50  WARNING         Removed 30 loci ( promoters ) because they contain missing values
2013-07-04 12:57:50   STATUS         Calculated PCA coordinates
2013-07-04 12:57:50   STATUS         Calculated MDS coordinates using manhattan distance
2013-07-04 12:57:50   STATUS         Calculated MDS coordinates using euclidean distance
2013-07-04 12:57:51  WARNING         Removed 15 loci ( cpgislands ) because they contain missing values
2013-07-04 12:57:51   STATUS         Calculated PCA coordinates
2013-07-04 12:57:51   STATUS         Calculated MDS coordinates using manhattan distance
2013-07-04 12:57:51   STATUS         Calculated MDS coordinates using euclidean distance
2013-07-04 12:57:51     INFO         Mapping 2 traits to point colors and types
2013-07-04 13:14:59     INFO         Principal components that explain at least 95 % of the total variance: 5
2013-07-04 13:14:59     INFO         Saved percentage of total variance to pca_variance_explained_1.csv
2013-07-04 13:15:03     INFO         Principal components that explain at least 95 % of the total variance: 5
2013-07-04 13:15:03     INFO         Saved percentage of total variance to pca_variance_explained_2.csv
2013-07-04 13:15:08     INFO         Principal components that explain at least 95 % of the total variance: 5
2013-07-04 13:15:08     INFO         Saved percentage of total variance to pca_variance_explained_3.csv
2013-07-04 13:15:12     INFO         Principal components that explain at least 95 % of the total variance: 5
2013-07-04 13:15:12     INFO         Saved percentage of total variance to pca_variance_explained_4.csv
2013-07-04 13:15:16     INFO         Principal components that explain at least 95 % of the total variance: 5
2013-07-04 13:15:16     INFO         Saved percentage of total variance to pca_variance_explained_5.csv
2013-07-04 13:15:20   STATUS         Created scatter plots and CDFs summarizing the reduced dimensional representations
2013-07-04 13:15:20   STATUS     COMPLETED Dimension Reduction Techniques
2013-07-04 13:15:20   STATUS     STARTED Tests for Associations
2013-07-04 13:15:20     INFO         Testing the following traits for associations: tumour site; tissue
2013-07-04 13:15:20   STATUS         Computed correlations between principal components and traits.
2013-07-04 13:15:20   STATUS         Computed pairwise correlations between traits.
2013-07-04 13:15:20   STATUS     COMPLETED Tests for Associations
2013-07-04 13:15:48   STATUS     STARTED Quality-associated Batch Effects
2013-07-04 13:15:48  WARNING         No quality information available
2013-07-04 13:15:48   STATUS     COMPLETED Quality-associated Batch Effects
2013-07-04 13:15:48     INFO     Initialized report index and saved to index.html
2013-07-04 13:15:49   STATUS     STARTED Methylation Profiles
2013-07-04 13:15:49     INFO         Designed color mappings for probe type and CGI status
2013-07-04 13:15:57   STATUS         STARTED Methylation Value Distributions - Sample Groups
2013-07-04 13:19:31   STATUS         COMPLETED Methylation Value Distributions - Sample Groups
2013-07-04 13:19:31   STATUS         STARTED Methylation Value Distributions - Probe Categories
2013-07-04 13:22:46   STATUS         COMPLETED Methylation Value Distributions - Probe Categories
2013-07-04 13:22:47   STATUS         STARTED Scatter Plots of Mean Beta vs Variance
2013-07-04 13:22:47     INFO             Sample subgroups are defined by: tumour site; tissue
2013-07-04 13:22:48  WARNING             Removed 10 loci with missing values in group all samples
2013-07-04 13:31:43  WARNING             Removed 1448 loci with missing values in group base of tongue (based on tumour site)
2013-07-04 13:40:36  WARNING             Removed 26 loci with missing values in group tonsil (based on tumour site)
2013-07-04 13:49:33  WARNING             Removed 56 loci with missing values in group HPV+ HNSCC tumor (based on tissue)
2013-07-04 13:58:28  WARNING             Removed 78 loci with missing values in group HPV- HNSCC tumor (based on tissue)
2013-07-04 14:07:20   STATUS             Created 20 scatter plots of methylation variance on the site level
2013-07-04 14:07:21  WARNING             Removed 1 loci with missing values in group all samples
2013-07-04 14:08:44  WARNING             Removed 159 loci with missing values in group base of tongue (based on tumour site)
2013-07-04 14:10:05  WARNING             Removed 2 loci with missing values in group tonsil (based on tumour site)
2013-07-04 14:11:26  WARNING             Removed 4 loci with missing values in group HPV+ HNSCC tumor (based on tissue)
2013-07-04 14:12:48  WARNING             Removed 7 loci with missing values in group HPV- HNSCC tumor (based on tissue)
2013-07-04 14:14:34  WARNING             Removed 9 loci with missing values in group base of tongue (based on tumour site)
2013-07-04 14:16:42  WARNING             Removed 8 loci with missing values in group base of tongue (based on tumour site)
2013-07-04 14:17:34  WARNING             Removed 1 loci with missing values in group HPV+ HNSCC tumor (based on tissue)
2013-07-04 14:18:49  WARNING             Removed 2 loci with missing values in group base of tongue (based on tumour site)
2013-07-04 14:20:26   STATUS             Created 40 scatter plots of methylation variance on the region level
2013-07-04 14:20:26   STATUS         COMPLETED Scatter Plots of Mean Beta vs Variance
2013-07-04 14:20:26   STATUS         STARTED Deviation Plots
2013-07-04 14:49:08   STATUS             Created 15 deviation plots on the site level
2013-07-04 15:04:01   STATUS             Created 20 deviation plots on the region level
2013-07-04 15:04:02   STATUS             Added summary table of variabilities
2013-07-04 15:04:02   STATUS         COMPLETED Deviation Plots
2013-07-04 15:04:02   STATUS         STARTED Sample Clustering
2013-07-04 15:04:02   STATUS             STARTED Agglomerative Hierarchical Clustering
2013-07-04 15:04:02   STATUS                 Performed clustering on sites using correlation as a distance metric
2013-07-04 15:04:02   STATUS                 Performed clustering on sites using manhattan as a distance metric
2013-07-04 15:04:03   STATUS                 Performed clustering on sites using euclidean as a distance metric
2013-07-04 15:04:03   STATUS                 Performed clustering on tiling using correlation as a distance metric
2013-07-04 15:04:03   STATUS                 Performed clustering on tiling using manhattan as a distance metric
2013-07-04 15:04:03   STATUS                 Performed clustering on tiling using euclidean as a distance metric
2013-07-04 15:04:03   STATUS                 Completed clustering for tiling
2013-07-04 15:04:03   STATUS                 Performed clustering on genes using correlation as a distance metric
2013-07-04 15:04:03   STATUS                 Performed clustering on genes using manhattan as a distance metric
2013-07-04 15:04:03   STATUS                 Performed clustering on genes using euclidean as a distance metric
2013-07-04 15:04:03   STATUS                 Completed clustering for genes
2013-07-04 15:04:03   STATUS                 Performed clustering on promoters using correlation as a distance metric
2013-07-04 15:04:03   STATUS                 Performed clustering on promoters using manhattan as a distance metric
2013-07-04 15:04:03   STATUS                 Performed clustering on promoters using euclidean as a distance metric
2013-07-04 15:04:03   STATUS                 Completed clustering for promoters
2013-07-04 15:04:03   STATUS                 Performed clustering on cpgislands using correlation as a distance metric
2013-07-04 15:04:03   STATUS                 Performed clustering on cpgislands using manhattan as a distance metric
2013-07-04 15:04:04   STATUS                 Performed clustering on cpgislands using euclidean as a distance metric
2013-07-04 15:04:04   STATUS                 Completed clustering for cpgislands
2013-07-04 15:04:04   STATUS             COMPLETED Agglomerative Hierarchical Clustering
2013-07-04 15:04:04   STATUS             STARTED Clustering Section
2013-07-04 15:04:05   STATUS                 STARTED Generating Heatmaps
2013-07-04 15:04:05   STATUS                     STARTED Region type: sites
2013-07-04 15:12:40   STATUS                     COMPLETED Region type: sites
2013-07-04 15:12:40   STATUS                     STARTED Region type: tiling
2013-07-04 15:21:19   STATUS                     COMPLETED Region type: tiling
2013-07-04 15:21:19   STATUS                     STARTED Region type: genes
2013-07-04 15:29:56   STATUS                     COMPLETED Region type: genes
2013-07-04 15:29:56   STATUS                     STARTED Region type: promoters
2013-07-04 15:38:33   STATUS                     COMPLETED Region type: promoters
2013-07-04 15:38:33   STATUS                     STARTED Region type: cpgislands
2013-07-04 15:47:09   STATUS                     COMPLETED Region type: cpgislands
2013-07-04 15:47:10   STATUS                     Created 360 heatmaps based on the clustering results
2013-07-04 15:47:10   STATUS                 COMPLETED Generating Heatmaps
2013-07-04 15:47:10   STATUS                 STARTED Adding Color Legends
2013-07-04 15:50:15   STATUS                 COMPLETED Adding Color Legends
2013-07-04 15:50:15   STATUS                 STARTED Estimating Optimal Numbers of Clusters
2013-07-04 15:51:21   STATUS                     Estimated number of clusters based on mean silhouette value
2013-07-04 15:51:21   STATUS                 COMPLETED Estimating Optimal Numbers of Clusters
2013-07-04 15:51:21   STATUS                 STARTED Overlapping Clusters with Sample Traits
2013-07-04 15:51:21   STATUS                     Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_1.csv
2013-07-04 15:51:21   STATUS                     Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_2.csv
2013-07-04 15:51:21   STATUS                     Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_3.csv
2013-07-04 15:51:21   STATUS                     Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_4.csv
2013-07-04 15:51:21   STATUS                     Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_5.csv
2013-07-04 15:52:26   STATUS                 COMPLETED Overlapping Clusters with Sample Traits
2013-07-04 15:52:26   STATUS             COMPLETED Clustering Section
2013-07-04 15:52:26   STATUS         COMPLETED Sample Clustering
2013-07-04 15:52:26   STATUS         STARTED Regional Methylation Profiling
2013-07-04 15:52:26   STATUS             STARTED Computing Regional Profiles Based on Binning
2013-07-04 15:52:26   STATUS                 STARTED Processing Region Type: genes
2013-07-04 16:03:01   STATUS                     Set region annotation and site membership
2013-07-04 16:04:02   STATUS                     Computed binned methylation values
2013-07-04 16:04:02   STATUS                 COMPLETED Processing Region Type: genes
2013-07-04 16:04:02   STATUS                 STARTED Processing Region Type: promoters
2013-07-04 16:14:38   STATUS                     Set region annotation and site membership
2013-07-04 16:15:29   STATUS                     Computed binned methylation values
2013-07-04 16:15:29   STATUS                 COMPLETED Processing Region Type: promoters
2013-07-04 16:15:29   STATUS                 STARTED Processing Region Type: cpgislands
2013-07-04 16:25:46   STATUS                     Set region annotation and site membership
2013-07-04 16:26:38   STATUS                     Computed binned methylation values
2013-07-04 16:26:38   STATUS                 COMPLETED Processing Region Type: cpgislands
2013-07-04 16:26:38   STATUS             COMPLETED Computing Regional Profiles Based on Binning
2013-07-04 16:26:38   STATUS             STARTED Creating a Corresponding Section in the Report
2013-07-04 16:26:38   STATUS                 Plotting region profiles for region genes and column tumour site ...
2013-07-04 16:28:31   STATUS                 Plotting region profiles for region genes and column tissue ...
2013-07-04 16:29:44   STATUS                 Plotting region profiles for region promoters and column tumour site ...
2013-07-04 16:30:31   STATUS                 Plotting region profiles for region promoters and column tissue ...
2013-07-04 16:31:15   STATUS                 Plotting region profiles for region cpgislands and column tumour site ...
2013-07-04 16:32:16   STATUS                 Plotting region profiles for region cpgislands and column tissue ...
2013-07-04 16:33:13   STATUS             COMPLETED Creating a Corresponding Section in the Report
2013-07-04 16:33:13   STATUS         COMPLETED Regional Methylation Profiling
2013-07-04 16:33:13   STATUS     COMPLETED Methylation Profiles
2013-07-04 16:33:13     INFO     Initialized report index and saved to index.html
2013-07-04 16:33:14   STATUS     STARTED Differential Methylation - Analysis
2013-07-04 16:33:14     INFO         Using 0 permutation tests
2013-07-04 16:33:14     INFO         Using columns: title,geo_accession,status,submission_date,last_update_date,type,channel_count,source_name_ch1,organism_ch1,molecule_ch1,extract_protocol_ch1,label_ch1,label_protocol_ch1,taxid_ch1,hyb_protocol,scan_protocol,description,data_processing,platform_id,contact_name,contact_email,contact_laboratory,contact_department,contact_institute,contact_address,contact_city,contact_zip/postal_code,contact_country,supplementary_file,data_row_count,tumour site,tissue
2013-07-04 16:33:14     INFO         Using region types: tiling,genes,promoters,cpgislands
2013-07-04 16:33:14   STATUS         STARTED Comparison Information: tumour site
2013-07-04 16:33:14   STATUS             STARTED Comparing base of tongue-tonsil
2013-07-04 16:33:14   STATUS                 STARTED Computing Differential Methylation Table (Site Level)
2013-07-04 16:33:21     INFO                     Some t-test p-values are NA. They are treated as 1 in FDR adjustment
2013-07-04 16:33:28   STATUS                 COMPLETED Computing Differential Methylation Table (Site Level)
2013-07-04 16:33:28   STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2013-07-04 16:45:21     INFO                     Some p-values are NA. They are treated as 1 in FDR adjustment
2013-07-04 16:45:21   STATUS                     Computed table for tiling
2013-07-04 16:48:07     INFO                     Some p-values are NA. They are treated as 1 in FDR adjustment
2013-07-04 16:48:07   STATUS                     Computed table for genes
2013-07-04 16:50:48     INFO                     Some p-values are NA. They are treated as 1 in FDR adjustment
2013-07-04 16:50:48   STATUS                     Computed table for promoters
2013-07-04 16:53:07     INFO                     Some p-values are NA. They are treated as 1 in FDR adjustment
2013-07-04 16:53:07   STATUS                     Computed table for cpgislands
2013-07-04 16:53:07   STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2013-07-04 16:53:07   STATUS             COMPLETED Comparing base of tongue-tonsil
2013-07-04 16:53:07   STATUS         COMPLETED Comparison Information: tumour site
2013-07-04 16:53:07   STATUS         STARTED Comparison Information: tissue
2013-07-04 16:53:07   STATUS             STARTED Comparing HPV+ HNSCC tumor-HPV- HNSCC tumor
2013-07-04 16:53:07   STATUS                 STARTED Computing Differential Methylation Table (Site Level)
2013-07-04 16:53:12     INFO                     Some t-test p-values are NA. They are treated as 1 in FDR adjustment
2013-07-04 16:53:17   STATUS                 COMPLETED Computing Differential Methylation Table (Site Level)
2013-07-04 16:53:17   STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2013-07-04 17:04:12     INFO                     Some p-values are NA. They are treated as 1 in FDR adjustment
2013-07-04 17:04:13   STATUS                     Computed table for tiling
2013-07-04 17:06:56   STATUS                     Computed table for genes
2013-07-04 17:09:29     INFO                     Some p-values are NA. They are treated as 1 in FDR adjustment
2013-07-04 17:09:29   STATUS                     Computed table for promoters
2013-07-04 17:11:43   STATUS                     Computed table for cpgislands
2013-07-04 17:11:43   STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2013-07-04 17:11:43   STATUS             COMPLETED Comparing HPV+ HNSCC tumor-HPV- HNSCC tumor
2013-07-04 17:11:43   STATUS         COMPLETED Comparison Information: tissue
2013-07-04 17:11:43     INFO         Skipping enrichment analysis of differentially methylated regions
2013-07-04 17:11:43   STATUS     COMPLETED Differential Methylation - Analysis
2013-07-04 17:11:43   STATUS     STARTED Differential Methylation - Report Generation
2013-07-04 17:11:43   STATUS         Added introductory section
2013-07-04 17:11:43   STATUS         STARTED Adding Site Level Information
2013-07-04 18:03:20   STATUS         COMPLETED Adding Site Level Information
2013-07-04 18:03:20   STATUS         STARTED Adding Region Level Information
2013-07-04 18:31:24   STATUS         COMPLETED Adding Region Level Information
2013-07-04 18:31:24   STATUS     COMPLETED Differential Methylation - Report Generation
2013-07-04 18:31:25     INFO     Initialized report index and saved to index.html
2013-07-04 18:31:25   STATUS     STARTED Data Export
2013-07-04 18:31:25   STATUS         STARTED Exporting RnBSet
2013-07-04 18:31:25   STATUS             STARTED Exporting sites
2013-07-04 18:31:25   STATUS                 STARTED Creating UCSC Track Hub -- bigBed
2013-07-04 18:31:25   STATUS                     STARTED Conversion to BED
2013-07-04 18:33:46   STATUS                     COMPLETED Conversion to BED
2013-07-04 18:33:46   STATUS                     STARTED Creating UCSC Track Hub
2013-07-04 18:34:06   STATUS                     COMPLETED Creating UCSC Track Hub
2013-07-04 18:34:06   STATUS                 COMPLETED Creating UCSC Track Hub -- bigBed
2013-07-04 18:34:06   STATUS                 STARTED Creating UCSC Track Hub -- bigWig
2013-07-04 18:34:06   STATUS                     STARTED Conversion to bedGraph
2013-07-04 18:36:10   STATUS                     COMPLETED Conversion to bedGraph
2013-07-04 18:36:10   STATUS                     STARTED Creating UCSC Track Hub
2013-07-04 18:36:28   STATUS                     COMPLETED Creating UCSC Track Hub
2013-07-04 18:36:28   STATUS                 COMPLETED Creating UCSC Track Hub -- bigWig
2013-07-04 18:36:28   STATUS             COMPLETED Exporting sites
2013-07-04 18:36:28   STATUS         COMPLETED Exporting RnBSet
2013-07-04 18:36:28   STATUS         STARTED Writing export report
2013-07-04 18:36:28   STATUS         COMPLETED Writing export report
2013-07-04 18:36:28   STATUS     COMPLETED Data Export
2013-07-04 18:36:28     INFO     Initialized report index and saved to index.html
2013-07-04 18:36:29   STATUS COMPLETED RnBeads Pipeline