Mercurial > repos > pavlo-lutsik > rnbeads
diff rnb.cloud.4.07.analysis.log @ 31:aad84663f9c2 draft
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| author | pavlo-lutsik |
|---|---|
| date | Fri, 05 Jul 2013 08:03:54 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnb.cloud.4.07.analysis.log Fri Jul 05 08:03:54 2013 -0400 @@ -0,0 +1,265 @@ +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 +