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31
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1 2013-07-04 12:48:18 STATUS STARTED RnBeads Pipeline
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2 2013-07-04 12:48:18 INFO Initialized report index and saved to index.html
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3 2013-07-04 12:48:18 STATUS STARTED Loading Data
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4 2013-07-04 12:48:18 STATUS STARTED Loading GEO Data Series
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5 2013-07-04 12:53:38 INFO Loaded 1 data series from GSE38268
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6 2013-07-04 12:53:38 INFO Extracted 6 samples from series 1
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7 2013-07-04 12:53:38 INFO Parsed characteristics_ch1 sample information
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8 2013-07-04 12:53:38 STATUS COMPLETED Loading GEO Data Series
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9 2013-07-04 12:54:49 STATUS Loaded data from GSE38268. Output object is of class RnBeadSet
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10 2013-07-04 12:54:50 STATUS Added data loading section
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11 2013-07-04 12:54:50 STATUS COMPLETED Loading Data
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12 2013-07-04 12:54:50 STATUS STARTED Normalization
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13 2013-07-04 12:54:50 WARNING Incompatible values for object and method. Changed the normalization method to "none"
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14 2013-07-04 12:54:50 WARNING Incompatible values for object and background correction flag. Disabled the background correction
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15 2013-07-04 12:54:50 STATUS Performed normalization with method "swan"
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16 2013-07-04 12:54:53 STATUS Added normalization section
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17 2013-07-04 12:54:53 STATUS COMPLETED Normalization
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18 2013-07-04 12:54:54 INFO Initialized report index and saved to index.html
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19 2013-07-04 12:54:54 STATUS STARTED Quality Control
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20 2013-07-04 12:54:54 STATUS STARTED Quality Control Section
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21 2013-07-04 12:54:54 INFO No quality information present in the dataset
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22 2013-07-04 12:54:54 STATUS COMPLETED Quality Control Section
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23 2013-07-04 12:54:54 STATUS COMPLETED Quality Control
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24 2013-07-04 12:54:54 STATUS STARTED Visualizing Sample Mixups
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25 2013-07-04 12:54:54 STATUS STARTED Mixups Visualization Section
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26 2013-07-04 12:55:15 STATUS Added SNP heatmap
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27 2013-07-04 12:55:15 STATUS COMPLETED Mixups Visualization Section
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28 2013-07-04 12:55:15 STATUS COMPLETED Visualizing Sample Mixups
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29 2013-07-04 12:55:15 INFO Initialized report index and saved to index.html
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30 2013-07-04 12:55:15 STATUS STARTED Filtering
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31 2013-07-04 12:55:23 STATUS STARTED Probe Context Removal
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32 2013-07-04 12:56:00 STATUS Removed 3156 probe(s) out of context
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33 2013-07-04 12:56:01 STATUS Saved removed sites to /mnt/galaxy/files/000/dataset_3_files/filtering_data/removed_sites_context.csv
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34 2013-07-04 12:56:01 STATUS Added a corresponding section to the report
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35 2013-07-04 12:56:01 STATUS COMPLETED Probe Context Removal
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36 2013-07-04 12:56:03 STATUS STARTED Removal of SNP-enriched Sites
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37 2013-07-04 12:56:38 STATUS Removed 18987 sites that overlap sites with more than 2 SNP(s)
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38 2013-07-04 12:56:38 STATUS Saved removed sites to /mnt/galaxy/files/000/dataset_3_files/filtering_data/removed_sites_snp.csv
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39 2013-07-04 12:56:38 STATUS Added a corresponding section to the report
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40 2013-07-04 12:56:38 STATUS COMPLETED Removal of SNP-enriched Sites
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41 2013-07-04 12:56:39 INFO Omitting Greedycut because detection p-values are missing
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42 2013-07-04 12:56:42 STATUS STARTED Summary of Filtering Procedures
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43 2013-07-04 12:56:46 STATUS Added summary table of removed and retained values
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44 2013-07-04 12:57:47 STATUS Added comparison between removed and retained beta values
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45 2013-07-04 12:57:47 STATUS COMPLETED Summary of Filtering Procedures
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46 2013-07-04 12:57:47 STATUS COMPLETED Filtering
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47 2013-07-04 12:57:47 INFO Initialized report index and saved to index.html
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48 2013-07-04 12:57:47 STATUS STARTED Dimension Reduction Techniques
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49 2013-07-04 12:57:48 WARNING Removed 4301 loci ( sites ) because they contain missing values
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50 2013-07-04 12:57:49 STATUS Calculated PCA coordinates
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51 2013-07-04 12:57:49 STATUS Calculated MDS coordinates using manhattan distance
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52 2013-07-04 12:57:49 STATUS Calculated MDS coordinates using euclidean distance
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53 2013-07-04 12:57:50 WARNING Removed 491 loci ( tiling ) because they contain missing values
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54 2013-07-04 12:57:50 STATUS Calculated PCA coordinates
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55 2013-07-04 12:57:50 STATUS Calculated MDS coordinates using manhattan distance
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56 2013-07-04 12:57:50 STATUS Calculated MDS coordinates using euclidean distance
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57 2013-07-04 12:57:50 WARNING Removed 25 loci ( genes ) because they contain missing values
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58 2013-07-04 12:57:50 STATUS Calculated PCA coordinates
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59 2013-07-04 12:57:50 STATUS Calculated MDS coordinates using manhattan distance
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60 2013-07-04 12:57:50 STATUS Calculated MDS coordinates using euclidean distance
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61 2013-07-04 12:57:50 WARNING Removed 30 loci ( promoters ) because they contain missing values
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62 2013-07-04 12:57:50 STATUS Calculated PCA coordinates
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63 2013-07-04 12:57:50 STATUS Calculated MDS coordinates using manhattan distance
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64 2013-07-04 12:57:50 STATUS Calculated MDS coordinates using euclidean distance
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65 2013-07-04 12:57:51 WARNING Removed 15 loci ( cpgislands ) because they contain missing values
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66 2013-07-04 12:57:51 STATUS Calculated PCA coordinates
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67 2013-07-04 12:57:51 STATUS Calculated MDS coordinates using manhattan distance
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68 2013-07-04 12:57:51 STATUS Calculated MDS coordinates using euclidean distance
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69 2013-07-04 12:57:51 INFO Mapping 2 traits to point colors and types
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70 2013-07-04 13:14:59 INFO Principal components that explain at least 95 % of the total variance: 5
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71 2013-07-04 13:14:59 INFO Saved percentage of total variance to pca_variance_explained_1.csv
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72 2013-07-04 13:15:03 INFO Principal components that explain at least 95 % of the total variance: 5
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73 2013-07-04 13:15:03 INFO Saved percentage of total variance to pca_variance_explained_2.csv
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74 2013-07-04 13:15:08 INFO Principal components that explain at least 95 % of the total variance: 5
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75 2013-07-04 13:15:08 INFO Saved percentage of total variance to pca_variance_explained_3.csv
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76 2013-07-04 13:15:12 INFO Principal components that explain at least 95 % of the total variance: 5
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77 2013-07-04 13:15:12 INFO Saved percentage of total variance to pca_variance_explained_4.csv
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78 2013-07-04 13:15:16 INFO Principal components that explain at least 95 % of the total variance: 5
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79 2013-07-04 13:15:16 INFO Saved percentage of total variance to pca_variance_explained_5.csv
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80 2013-07-04 13:15:20 STATUS Created scatter plots and CDFs summarizing the reduced dimensional representations
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81 2013-07-04 13:15:20 STATUS COMPLETED Dimension Reduction Techniques
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82 2013-07-04 13:15:20 STATUS STARTED Tests for Associations
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83 2013-07-04 13:15:20 INFO Testing the following traits for associations: tumour site; tissue
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84 2013-07-04 13:15:20 STATUS Computed correlations between principal components and traits.
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85 2013-07-04 13:15:20 STATUS Computed pairwise correlations between traits.
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86 2013-07-04 13:15:20 STATUS COMPLETED Tests for Associations
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87 2013-07-04 13:15:48 STATUS STARTED Quality-associated Batch Effects
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88 2013-07-04 13:15:48 WARNING No quality information available
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89 2013-07-04 13:15:48 STATUS COMPLETED Quality-associated Batch Effects
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90 2013-07-04 13:15:48 INFO Initialized report index and saved to index.html
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91 2013-07-04 13:15:49 STATUS STARTED Methylation Profiles
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92 2013-07-04 13:15:49 INFO Designed color mappings for probe type and CGI status
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93 2013-07-04 13:15:57 STATUS STARTED Methylation Value Distributions - Sample Groups
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94 2013-07-04 13:19:31 STATUS COMPLETED Methylation Value Distributions - Sample Groups
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95 2013-07-04 13:19:31 STATUS STARTED Methylation Value Distributions - Probe Categories
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96 2013-07-04 13:22:46 STATUS COMPLETED Methylation Value Distributions - Probe Categories
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97 2013-07-04 13:22:47 STATUS STARTED Scatter Plots of Mean Beta vs Variance
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98 2013-07-04 13:22:47 INFO Sample subgroups are defined by: tumour site; tissue
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99 2013-07-04 13:22:48 WARNING Removed 10 loci with missing values in group all samples
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100 2013-07-04 13:31:43 WARNING Removed 1448 loci with missing values in group base of tongue (based on tumour site)
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101 2013-07-04 13:40:36 WARNING Removed 26 loci with missing values in group tonsil (based on tumour site)
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102 2013-07-04 13:49:33 WARNING Removed 56 loci with missing values in group HPV+ HNSCC tumor (based on tissue)
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103 2013-07-04 13:58:28 WARNING Removed 78 loci with missing values in group HPV- HNSCC tumor (based on tissue)
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104 2013-07-04 14:07:20 STATUS Created 20 scatter plots of methylation variance on the site level
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105 2013-07-04 14:07:21 WARNING Removed 1 loci with missing values in group all samples
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106 2013-07-04 14:08:44 WARNING Removed 159 loci with missing values in group base of tongue (based on tumour site)
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107 2013-07-04 14:10:05 WARNING Removed 2 loci with missing values in group tonsil (based on tumour site)
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108 2013-07-04 14:11:26 WARNING Removed 4 loci with missing values in group HPV+ HNSCC tumor (based on tissue)
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109 2013-07-04 14:12:48 WARNING Removed 7 loci with missing values in group HPV- HNSCC tumor (based on tissue)
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110 2013-07-04 14:14:34 WARNING Removed 9 loci with missing values in group base of tongue (based on tumour site)
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111 2013-07-04 14:16:42 WARNING Removed 8 loci with missing values in group base of tongue (based on tumour site)
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112 2013-07-04 14:17:34 WARNING Removed 1 loci with missing values in group HPV+ HNSCC tumor (based on tissue)
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113 2013-07-04 14:18:49 WARNING Removed 2 loci with missing values in group base of tongue (based on tumour site)
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114 2013-07-04 14:20:26 STATUS Created 40 scatter plots of methylation variance on the region level
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115 2013-07-04 14:20:26 STATUS COMPLETED Scatter Plots of Mean Beta vs Variance
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116 2013-07-04 14:20:26 STATUS STARTED Deviation Plots
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117 2013-07-04 14:49:08 STATUS Created 15 deviation plots on the site level
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118 2013-07-04 15:04:01 STATUS Created 20 deviation plots on the region level
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119 2013-07-04 15:04:02 STATUS Added summary table of variabilities
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120 2013-07-04 15:04:02 STATUS COMPLETED Deviation Plots
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121 2013-07-04 15:04:02 STATUS STARTED Sample Clustering
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122 2013-07-04 15:04:02 STATUS STARTED Agglomerative Hierarchical Clustering
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123 2013-07-04 15:04:02 STATUS Performed clustering on sites using correlation as a distance metric
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124 2013-07-04 15:04:02 STATUS Performed clustering on sites using manhattan as a distance metric
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125 2013-07-04 15:04:03 STATUS Performed clustering on sites using euclidean as a distance metric
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126 2013-07-04 15:04:03 STATUS Performed clustering on tiling using correlation as a distance metric
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127 2013-07-04 15:04:03 STATUS Performed clustering on tiling using manhattan as a distance metric
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128 2013-07-04 15:04:03 STATUS Performed clustering on tiling using euclidean as a distance metric
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129 2013-07-04 15:04:03 STATUS Completed clustering for tiling
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130 2013-07-04 15:04:03 STATUS Performed clustering on genes using correlation as a distance metric
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131 2013-07-04 15:04:03 STATUS Performed clustering on genes using manhattan as a distance metric
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132 2013-07-04 15:04:03 STATUS Performed clustering on genes using euclidean as a distance metric
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133 2013-07-04 15:04:03 STATUS Completed clustering for genes
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134 2013-07-04 15:04:03 STATUS Performed clustering on promoters using correlation as a distance metric
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135 2013-07-04 15:04:03 STATUS Performed clustering on promoters using manhattan as a distance metric
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136 2013-07-04 15:04:03 STATUS Performed clustering on promoters using euclidean as a distance metric
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137 2013-07-04 15:04:03 STATUS Completed clustering for promoters
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138 2013-07-04 15:04:03 STATUS Performed clustering on cpgislands using correlation as a distance metric
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139 2013-07-04 15:04:03 STATUS Performed clustering on cpgislands using manhattan as a distance metric
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140 2013-07-04 15:04:04 STATUS Performed clustering on cpgislands using euclidean as a distance metric
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141 2013-07-04 15:04:04 STATUS Completed clustering for cpgislands
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142 2013-07-04 15:04:04 STATUS COMPLETED Agglomerative Hierarchical Clustering
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143 2013-07-04 15:04:04 STATUS STARTED Clustering Section
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144 2013-07-04 15:04:05 STATUS STARTED Generating Heatmaps
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145 2013-07-04 15:04:05 STATUS STARTED Region type: sites
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146 2013-07-04 15:12:40 STATUS COMPLETED Region type: sites
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147 2013-07-04 15:12:40 STATUS STARTED Region type: tiling
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148 2013-07-04 15:21:19 STATUS COMPLETED Region type: tiling
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149 2013-07-04 15:21:19 STATUS STARTED Region type: genes
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150 2013-07-04 15:29:56 STATUS COMPLETED Region type: genes
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151 2013-07-04 15:29:56 STATUS STARTED Region type: promoters
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152 2013-07-04 15:38:33 STATUS COMPLETED Region type: promoters
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153 2013-07-04 15:38:33 STATUS STARTED Region type: cpgislands
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154 2013-07-04 15:47:09 STATUS COMPLETED Region type: cpgislands
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155 2013-07-04 15:47:10 STATUS Created 360 heatmaps based on the clustering results
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156 2013-07-04 15:47:10 STATUS COMPLETED Generating Heatmaps
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157 2013-07-04 15:47:10 STATUS STARTED Adding Color Legends
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158 2013-07-04 15:50:15 STATUS COMPLETED Adding Color Legends
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159 2013-07-04 15:50:15 STATUS STARTED Estimating Optimal Numbers of Clusters
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160 2013-07-04 15:51:21 STATUS Estimated number of clusters based on mean silhouette value
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161 2013-07-04 15:51:21 STATUS COMPLETED Estimating Optimal Numbers of Clusters
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162 2013-07-04 15:51:21 STATUS STARTED Overlapping Clusters with Sample Traits
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163 2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_1.csv
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164 2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_2.csv
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165 2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_3.csv
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166 2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_4.csv
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167 2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_5.csv
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168 2013-07-04 15:52:26 STATUS COMPLETED Overlapping Clusters with Sample Traits
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169 2013-07-04 15:52:26 STATUS COMPLETED Clustering Section
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170 2013-07-04 15:52:26 STATUS COMPLETED Sample Clustering
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171 2013-07-04 15:52:26 STATUS STARTED Regional Methylation Profiling
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172 2013-07-04 15:52:26 STATUS STARTED Computing Regional Profiles Based on Binning
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173 2013-07-04 15:52:26 STATUS STARTED Processing Region Type: genes
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174 2013-07-04 16:03:01 STATUS Set region annotation and site membership
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175 2013-07-04 16:04:02 STATUS Computed binned methylation values
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176 2013-07-04 16:04:02 STATUS COMPLETED Processing Region Type: genes
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177 2013-07-04 16:04:02 STATUS STARTED Processing Region Type: promoters
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178 2013-07-04 16:14:38 STATUS Set region annotation and site membership
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179 2013-07-04 16:15:29 STATUS Computed binned methylation values
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180 2013-07-04 16:15:29 STATUS COMPLETED Processing Region Type: promoters
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181 2013-07-04 16:15:29 STATUS STARTED Processing Region Type: cpgislands
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182 2013-07-04 16:25:46 STATUS Set region annotation and site membership
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183 2013-07-04 16:26:38 STATUS Computed binned methylation values
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184 2013-07-04 16:26:38 STATUS COMPLETED Processing Region Type: cpgislands
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185 2013-07-04 16:26:38 STATUS COMPLETED Computing Regional Profiles Based on Binning
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186 2013-07-04 16:26:38 STATUS STARTED Creating a Corresponding Section in the Report
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187 2013-07-04 16:26:38 STATUS Plotting region profiles for region genes and column tumour site ...
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188 2013-07-04 16:28:31 STATUS Plotting region profiles for region genes and column tissue ...
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189 2013-07-04 16:29:44 STATUS Plotting region profiles for region promoters and column tumour site ...
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190 2013-07-04 16:30:31 STATUS Plotting region profiles for region promoters and column tissue ...
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191 2013-07-04 16:31:15 STATUS Plotting region profiles for region cpgislands and column tumour site ...
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192 2013-07-04 16:32:16 STATUS Plotting region profiles for region cpgislands and column tissue ...
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193 2013-07-04 16:33:13 STATUS COMPLETED Creating a Corresponding Section in the Report
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194 2013-07-04 16:33:13 STATUS COMPLETED Regional Methylation Profiling
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195 2013-07-04 16:33:13 STATUS COMPLETED Methylation Profiles
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196 2013-07-04 16:33:13 INFO Initialized report index and saved to index.html
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197 2013-07-04 16:33:14 STATUS STARTED Differential Methylation - Analysis
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198 2013-07-04 16:33:14 INFO Using 0 permutation tests
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199 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
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200 2013-07-04 16:33:14 INFO Using region types: tiling,genes,promoters,cpgislands
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201 2013-07-04 16:33:14 STATUS STARTED Comparison Information: tumour site
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202 2013-07-04 16:33:14 STATUS STARTED Comparing base of tongue-tonsil
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203 2013-07-04 16:33:14 STATUS STARTED Computing Differential Methylation Table (Site Level)
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204 2013-07-04 16:33:21 INFO Some t-test p-values are NA. They are treated as 1 in FDR adjustment
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205 2013-07-04 16:33:28 STATUS COMPLETED Computing Differential Methylation Table (Site Level)
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206 2013-07-04 16:33:28 STATUS STARTED Computing Differential Methylation Tables (Region Level)
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207 2013-07-04 16:45:21 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
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208 2013-07-04 16:45:21 STATUS Computed table for tiling
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209 2013-07-04 16:48:07 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
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210 2013-07-04 16:48:07 STATUS Computed table for genes
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211 2013-07-04 16:50:48 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
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212 2013-07-04 16:50:48 STATUS Computed table for promoters
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213 2013-07-04 16:53:07 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
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214 2013-07-04 16:53:07 STATUS Computed table for cpgislands
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215 2013-07-04 16:53:07 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
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216 2013-07-04 16:53:07 STATUS COMPLETED Comparing base of tongue-tonsil
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217 2013-07-04 16:53:07 STATUS COMPLETED Comparison Information: tumour site
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218 2013-07-04 16:53:07 STATUS STARTED Comparison Information: tissue
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219 2013-07-04 16:53:07 STATUS STARTED Comparing HPV+ HNSCC tumor-HPV- HNSCC tumor
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220 2013-07-04 16:53:07 STATUS STARTED Computing Differential Methylation Table (Site Level)
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221 2013-07-04 16:53:12 INFO Some t-test p-values are NA. They are treated as 1 in FDR adjustment
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222 2013-07-04 16:53:17 STATUS COMPLETED Computing Differential Methylation Table (Site Level)
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223 2013-07-04 16:53:17 STATUS STARTED Computing Differential Methylation Tables (Region Level)
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224 2013-07-04 17:04:12 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
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225 2013-07-04 17:04:13 STATUS Computed table for tiling
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226 2013-07-04 17:06:56 STATUS Computed table for genes
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227 2013-07-04 17:09:29 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
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228 2013-07-04 17:09:29 STATUS Computed table for promoters
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229 2013-07-04 17:11:43 STATUS Computed table for cpgislands
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230 2013-07-04 17:11:43 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
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231 2013-07-04 17:11:43 STATUS COMPLETED Comparing HPV+ HNSCC tumor-HPV- HNSCC tumor
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232 2013-07-04 17:11:43 STATUS COMPLETED Comparison Information: tissue
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233 2013-07-04 17:11:43 INFO Skipping enrichment analysis of differentially methylated regions
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234 2013-07-04 17:11:43 STATUS COMPLETED Differential Methylation - Analysis
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235 2013-07-04 17:11:43 STATUS STARTED Differential Methylation - Report Generation
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236 2013-07-04 17:11:43 STATUS Added introductory section
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237 2013-07-04 17:11:43 STATUS STARTED Adding Site Level Information
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238 2013-07-04 18:03:20 STATUS COMPLETED Adding Site Level Information
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239 2013-07-04 18:03:20 STATUS STARTED Adding Region Level Information
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240 2013-07-04 18:31:24 STATUS COMPLETED Adding Region Level Information
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241 2013-07-04 18:31:24 STATUS COMPLETED Differential Methylation - Report Generation
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242 2013-07-04 18:31:25 INFO Initialized report index and saved to index.html
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243 2013-07-04 18:31:25 STATUS STARTED Data Export
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244 2013-07-04 18:31:25 STATUS STARTED Exporting RnBSet
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245 2013-07-04 18:31:25 STATUS STARTED Exporting sites
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246 2013-07-04 18:31:25 STATUS STARTED Creating UCSC Track Hub -- bigBed
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247 2013-07-04 18:31:25 STATUS STARTED Conversion to BED
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248 2013-07-04 18:33:46 STATUS COMPLETED Conversion to BED
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249 2013-07-04 18:33:46 STATUS STARTED Creating UCSC Track Hub
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250 2013-07-04 18:34:06 STATUS COMPLETED Creating UCSC Track Hub
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251 2013-07-04 18:34:06 STATUS COMPLETED Creating UCSC Track Hub -- bigBed
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252 2013-07-04 18:34:06 STATUS STARTED Creating UCSC Track Hub -- bigWig
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253 2013-07-04 18:34:06 STATUS STARTED Conversion to bedGraph
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254 2013-07-04 18:36:10 STATUS COMPLETED Conversion to bedGraph
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255 2013-07-04 18:36:10 STATUS STARTED Creating UCSC Track Hub
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256 2013-07-04 18:36:28 STATUS COMPLETED Creating UCSC Track Hub
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257 2013-07-04 18:36:28 STATUS COMPLETED Creating UCSC Track Hub -- bigWig
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258 2013-07-04 18:36:28 STATUS COMPLETED Exporting sites
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259 2013-07-04 18:36:28 STATUS COMPLETED Exporting RnBSet
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260 2013-07-04 18:36:28 STATUS STARTED Writing export report
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261 2013-07-04 18:36:28 STATUS COMPLETED Writing export report
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262 2013-07-04 18:36:28 STATUS COMPLETED Data Export
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263 2013-07-04 18:36:28 INFO Initialized report index and saved to index.html
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264 2013-07-04 18:36:29 STATUS COMPLETED RnBeads Pipeline
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265
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