comparison 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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30:afb06b3416d8 31:aad84663f9c2
1 2013-07-04 12:48:18 STATUS STARTED RnBeads Pipeline
2 2013-07-04 12:48:18 INFO Initialized report index and saved to index.html
3 2013-07-04 12:48:18 STATUS STARTED Loading Data
4 2013-07-04 12:48:18 STATUS STARTED Loading GEO Data Series
5 2013-07-04 12:53:38 INFO Loaded 1 data series from GSE38268
6 2013-07-04 12:53:38 INFO Extracted 6 samples from series 1
7 2013-07-04 12:53:38 INFO Parsed characteristics_ch1 sample information
8 2013-07-04 12:53:38 STATUS COMPLETED Loading GEO Data Series
9 2013-07-04 12:54:49 STATUS Loaded data from GSE38268. Output object is of class RnBeadSet
10 2013-07-04 12:54:50 STATUS Added data loading section
11 2013-07-04 12:54:50 STATUS COMPLETED Loading Data
12 2013-07-04 12:54:50 STATUS STARTED Normalization
13 2013-07-04 12:54:50 WARNING Incompatible values for object and method. Changed the normalization method to "none"
14 2013-07-04 12:54:50 WARNING Incompatible values for object and background correction flag. Disabled the background correction
15 2013-07-04 12:54:50 STATUS Performed normalization with method "swan"
16 2013-07-04 12:54:53 STATUS Added normalization section
17 2013-07-04 12:54:53 STATUS COMPLETED Normalization
18 2013-07-04 12:54:54 INFO Initialized report index and saved to index.html
19 2013-07-04 12:54:54 STATUS STARTED Quality Control
20 2013-07-04 12:54:54 STATUS STARTED Quality Control Section
21 2013-07-04 12:54:54 INFO No quality information present in the dataset
22 2013-07-04 12:54:54 STATUS COMPLETED Quality Control Section
23 2013-07-04 12:54:54 STATUS COMPLETED Quality Control
24 2013-07-04 12:54:54 STATUS STARTED Visualizing Sample Mixups
25 2013-07-04 12:54:54 STATUS STARTED Mixups Visualization Section
26 2013-07-04 12:55:15 STATUS Added SNP heatmap
27 2013-07-04 12:55:15 STATUS COMPLETED Mixups Visualization Section
28 2013-07-04 12:55:15 STATUS COMPLETED Visualizing Sample Mixups
29 2013-07-04 12:55:15 INFO Initialized report index and saved to index.html
30 2013-07-04 12:55:15 STATUS STARTED Filtering
31 2013-07-04 12:55:23 STATUS STARTED Probe Context Removal
32 2013-07-04 12:56:00 STATUS Removed 3156 probe(s) out of context
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
34 2013-07-04 12:56:01 STATUS Added a corresponding section to the report
35 2013-07-04 12:56:01 STATUS COMPLETED Probe Context Removal
36 2013-07-04 12:56:03 STATUS STARTED Removal of SNP-enriched Sites
37 2013-07-04 12:56:38 STATUS Removed 18987 sites that overlap sites with more than 2 SNP(s)
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
39 2013-07-04 12:56:38 STATUS Added a corresponding section to the report
40 2013-07-04 12:56:38 STATUS COMPLETED Removal of SNP-enriched Sites
41 2013-07-04 12:56:39 INFO Omitting Greedycut because detection p-values are missing
42 2013-07-04 12:56:42 STATUS STARTED Summary of Filtering Procedures
43 2013-07-04 12:56:46 STATUS Added summary table of removed and retained values
44 2013-07-04 12:57:47 STATUS Added comparison between removed and retained beta values
45 2013-07-04 12:57:47 STATUS COMPLETED Summary of Filtering Procedures
46 2013-07-04 12:57:47 STATUS COMPLETED Filtering
47 2013-07-04 12:57:47 INFO Initialized report index and saved to index.html
48 2013-07-04 12:57:47 STATUS STARTED Dimension Reduction Techniques
49 2013-07-04 12:57:48 WARNING Removed 4301 loci ( sites ) because they contain missing values
50 2013-07-04 12:57:49 STATUS Calculated PCA coordinates
51 2013-07-04 12:57:49 STATUS Calculated MDS coordinates using manhattan distance
52 2013-07-04 12:57:49 STATUS Calculated MDS coordinates using euclidean distance
53 2013-07-04 12:57:50 WARNING Removed 491 loci ( tiling ) because they contain missing values
54 2013-07-04 12:57:50 STATUS Calculated PCA coordinates
55 2013-07-04 12:57:50 STATUS Calculated MDS coordinates using manhattan distance
56 2013-07-04 12:57:50 STATUS Calculated MDS coordinates using euclidean distance
57 2013-07-04 12:57:50 WARNING Removed 25 loci ( genes ) because they contain missing values
58 2013-07-04 12:57:50 STATUS Calculated PCA coordinates
59 2013-07-04 12:57:50 STATUS Calculated MDS coordinates using manhattan distance
60 2013-07-04 12:57:50 STATUS Calculated MDS coordinates using euclidean distance
61 2013-07-04 12:57:50 WARNING Removed 30 loci ( promoters ) because they contain missing values
62 2013-07-04 12:57:50 STATUS Calculated PCA coordinates
63 2013-07-04 12:57:50 STATUS Calculated MDS coordinates using manhattan distance
64 2013-07-04 12:57:50 STATUS Calculated MDS coordinates using euclidean distance
65 2013-07-04 12:57:51 WARNING Removed 15 loci ( cpgislands ) because they contain missing values
66 2013-07-04 12:57:51 STATUS Calculated PCA coordinates
67 2013-07-04 12:57:51 STATUS Calculated MDS coordinates using manhattan distance
68 2013-07-04 12:57:51 STATUS Calculated MDS coordinates using euclidean distance
69 2013-07-04 12:57:51 INFO Mapping 2 traits to point colors and types
70 2013-07-04 13:14:59 INFO Principal components that explain at least 95 % of the total variance: 5
71 2013-07-04 13:14:59 INFO Saved percentage of total variance to pca_variance_explained_1.csv
72 2013-07-04 13:15:03 INFO Principal components that explain at least 95 % of the total variance: 5
73 2013-07-04 13:15:03 INFO Saved percentage of total variance to pca_variance_explained_2.csv
74 2013-07-04 13:15:08 INFO Principal components that explain at least 95 % of the total variance: 5
75 2013-07-04 13:15:08 INFO Saved percentage of total variance to pca_variance_explained_3.csv
76 2013-07-04 13:15:12 INFO Principal components that explain at least 95 % of the total variance: 5
77 2013-07-04 13:15:12 INFO Saved percentage of total variance to pca_variance_explained_4.csv
78 2013-07-04 13:15:16 INFO Principal components that explain at least 95 % of the total variance: 5
79 2013-07-04 13:15:16 INFO Saved percentage of total variance to pca_variance_explained_5.csv
80 2013-07-04 13:15:20 STATUS Created scatter plots and CDFs summarizing the reduced dimensional representations
81 2013-07-04 13:15:20 STATUS COMPLETED Dimension Reduction Techniques
82 2013-07-04 13:15:20 STATUS STARTED Tests for Associations
83 2013-07-04 13:15:20 INFO Testing the following traits for associations: tumour site; tissue
84 2013-07-04 13:15:20 STATUS Computed correlations between principal components and traits.
85 2013-07-04 13:15:20 STATUS Computed pairwise correlations between traits.
86 2013-07-04 13:15:20 STATUS COMPLETED Tests for Associations
87 2013-07-04 13:15:48 STATUS STARTED Quality-associated Batch Effects
88 2013-07-04 13:15:48 WARNING No quality information available
89 2013-07-04 13:15:48 STATUS COMPLETED Quality-associated Batch Effects
90 2013-07-04 13:15:48 INFO Initialized report index and saved to index.html
91 2013-07-04 13:15:49 STATUS STARTED Methylation Profiles
92 2013-07-04 13:15:49 INFO Designed color mappings for probe type and CGI status
93 2013-07-04 13:15:57 STATUS STARTED Methylation Value Distributions - Sample Groups
94 2013-07-04 13:19:31 STATUS COMPLETED Methylation Value Distributions - Sample Groups
95 2013-07-04 13:19:31 STATUS STARTED Methylation Value Distributions - Probe Categories
96 2013-07-04 13:22:46 STATUS COMPLETED Methylation Value Distributions - Probe Categories
97 2013-07-04 13:22:47 STATUS STARTED Scatter Plots of Mean Beta vs Variance
98 2013-07-04 13:22:47 INFO Sample subgroups are defined by: tumour site; tissue
99 2013-07-04 13:22:48 WARNING Removed 10 loci with missing values in group all samples
100 2013-07-04 13:31:43 WARNING Removed 1448 loci with missing values in group base of tongue (based on tumour site)
101 2013-07-04 13:40:36 WARNING Removed 26 loci with missing values in group tonsil (based on tumour site)
102 2013-07-04 13:49:33 WARNING Removed 56 loci with missing values in group HPV+ HNSCC tumor (based on tissue)
103 2013-07-04 13:58:28 WARNING Removed 78 loci with missing values in group HPV- HNSCC tumor (based on tissue)
104 2013-07-04 14:07:20 STATUS Created 20 scatter plots of methylation variance on the site level
105 2013-07-04 14:07:21 WARNING Removed 1 loci with missing values in group all samples
106 2013-07-04 14:08:44 WARNING Removed 159 loci with missing values in group base of tongue (based on tumour site)
107 2013-07-04 14:10:05 WARNING Removed 2 loci with missing values in group tonsil (based on tumour site)
108 2013-07-04 14:11:26 WARNING Removed 4 loci with missing values in group HPV+ HNSCC tumor (based on tissue)
109 2013-07-04 14:12:48 WARNING Removed 7 loci with missing values in group HPV- HNSCC tumor (based on tissue)
110 2013-07-04 14:14:34 WARNING Removed 9 loci with missing values in group base of tongue (based on tumour site)
111 2013-07-04 14:16:42 WARNING Removed 8 loci with missing values in group base of tongue (based on tumour site)
112 2013-07-04 14:17:34 WARNING Removed 1 loci with missing values in group HPV+ HNSCC tumor (based on tissue)
113 2013-07-04 14:18:49 WARNING Removed 2 loci with missing values in group base of tongue (based on tumour site)
114 2013-07-04 14:20:26 STATUS Created 40 scatter plots of methylation variance on the region level
115 2013-07-04 14:20:26 STATUS COMPLETED Scatter Plots of Mean Beta vs Variance
116 2013-07-04 14:20:26 STATUS STARTED Deviation Plots
117 2013-07-04 14:49:08 STATUS Created 15 deviation plots on the site level
118 2013-07-04 15:04:01 STATUS Created 20 deviation plots on the region level
119 2013-07-04 15:04:02 STATUS Added summary table of variabilities
120 2013-07-04 15:04:02 STATUS COMPLETED Deviation Plots
121 2013-07-04 15:04:02 STATUS STARTED Sample Clustering
122 2013-07-04 15:04:02 STATUS STARTED Agglomerative Hierarchical Clustering
123 2013-07-04 15:04:02 STATUS Performed clustering on sites using correlation as a distance metric
124 2013-07-04 15:04:02 STATUS Performed clustering on sites using manhattan as a distance metric
125 2013-07-04 15:04:03 STATUS Performed clustering on sites using euclidean as a distance metric
126 2013-07-04 15:04:03 STATUS Performed clustering on tiling using correlation as a distance metric
127 2013-07-04 15:04:03 STATUS Performed clustering on tiling using manhattan as a distance metric
128 2013-07-04 15:04:03 STATUS Performed clustering on tiling using euclidean as a distance metric
129 2013-07-04 15:04:03 STATUS Completed clustering for tiling
130 2013-07-04 15:04:03 STATUS Performed clustering on genes using correlation as a distance metric
131 2013-07-04 15:04:03 STATUS Performed clustering on genes using manhattan as a distance metric
132 2013-07-04 15:04:03 STATUS Performed clustering on genes using euclidean as a distance metric
133 2013-07-04 15:04:03 STATUS Completed clustering for genes
134 2013-07-04 15:04:03 STATUS Performed clustering on promoters using correlation as a distance metric
135 2013-07-04 15:04:03 STATUS Performed clustering on promoters using manhattan as a distance metric
136 2013-07-04 15:04:03 STATUS Performed clustering on promoters using euclidean as a distance metric
137 2013-07-04 15:04:03 STATUS Completed clustering for promoters
138 2013-07-04 15:04:03 STATUS Performed clustering on cpgislands using correlation as a distance metric
139 2013-07-04 15:04:03 STATUS Performed clustering on cpgislands using manhattan as a distance metric
140 2013-07-04 15:04:04 STATUS Performed clustering on cpgislands using euclidean as a distance metric
141 2013-07-04 15:04:04 STATUS Completed clustering for cpgislands
142 2013-07-04 15:04:04 STATUS COMPLETED Agglomerative Hierarchical Clustering
143 2013-07-04 15:04:04 STATUS STARTED Clustering Section
144 2013-07-04 15:04:05 STATUS STARTED Generating Heatmaps
145 2013-07-04 15:04:05 STATUS STARTED Region type: sites
146 2013-07-04 15:12:40 STATUS COMPLETED Region type: sites
147 2013-07-04 15:12:40 STATUS STARTED Region type: tiling
148 2013-07-04 15:21:19 STATUS COMPLETED Region type: tiling
149 2013-07-04 15:21:19 STATUS STARTED Region type: genes
150 2013-07-04 15:29:56 STATUS COMPLETED Region type: genes
151 2013-07-04 15:29:56 STATUS STARTED Region type: promoters
152 2013-07-04 15:38:33 STATUS COMPLETED Region type: promoters
153 2013-07-04 15:38:33 STATUS STARTED Region type: cpgislands
154 2013-07-04 15:47:09 STATUS COMPLETED Region type: cpgislands
155 2013-07-04 15:47:10 STATUS Created 360 heatmaps based on the clustering results
156 2013-07-04 15:47:10 STATUS COMPLETED Generating Heatmaps
157 2013-07-04 15:47:10 STATUS STARTED Adding Color Legends
158 2013-07-04 15:50:15 STATUS COMPLETED Adding Color Legends
159 2013-07-04 15:50:15 STATUS STARTED Estimating Optimal Numbers of Clusters
160 2013-07-04 15:51:21 STATUS Estimated number of clusters based on mean silhouette value
161 2013-07-04 15:51:21 STATUS COMPLETED Estimating Optimal Numbers of Clusters
162 2013-07-04 15:51:21 STATUS STARTED Overlapping Clusters with Sample Traits
163 2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_1.csv
164 2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_2.csv
165 2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_3.csv
166 2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_4.csv
167 2013-07-04 15:51:21 STATUS Computed adjusted rand indices and saved to profiles_data/adjusted_rand_indices_5.csv
168 2013-07-04 15:52:26 STATUS COMPLETED Overlapping Clusters with Sample Traits
169 2013-07-04 15:52:26 STATUS COMPLETED Clustering Section
170 2013-07-04 15:52:26 STATUS COMPLETED Sample Clustering
171 2013-07-04 15:52:26 STATUS STARTED Regional Methylation Profiling
172 2013-07-04 15:52:26 STATUS STARTED Computing Regional Profiles Based on Binning
173 2013-07-04 15:52:26 STATUS STARTED Processing Region Type: genes
174 2013-07-04 16:03:01 STATUS Set region annotation and site membership
175 2013-07-04 16:04:02 STATUS Computed binned methylation values
176 2013-07-04 16:04:02 STATUS COMPLETED Processing Region Type: genes
177 2013-07-04 16:04:02 STATUS STARTED Processing Region Type: promoters
178 2013-07-04 16:14:38 STATUS Set region annotation and site membership
179 2013-07-04 16:15:29 STATUS Computed binned methylation values
180 2013-07-04 16:15:29 STATUS COMPLETED Processing Region Type: promoters
181 2013-07-04 16:15:29 STATUS STARTED Processing Region Type: cpgislands
182 2013-07-04 16:25:46 STATUS Set region annotation and site membership
183 2013-07-04 16:26:38 STATUS Computed binned methylation values
184 2013-07-04 16:26:38 STATUS COMPLETED Processing Region Type: cpgislands
185 2013-07-04 16:26:38 STATUS COMPLETED Computing Regional Profiles Based on Binning
186 2013-07-04 16:26:38 STATUS STARTED Creating a Corresponding Section in the Report
187 2013-07-04 16:26:38 STATUS Plotting region profiles for region genes and column tumour site ...
188 2013-07-04 16:28:31 STATUS Plotting region profiles for region genes and column tissue ...
189 2013-07-04 16:29:44 STATUS Plotting region profiles for region promoters and column tumour site ...
190 2013-07-04 16:30:31 STATUS Plotting region profiles for region promoters and column tissue ...
191 2013-07-04 16:31:15 STATUS Plotting region profiles for region cpgislands and column tumour site ...
192 2013-07-04 16:32:16 STATUS Plotting region profiles for region cpgislands and column tissue ...
193 2013-07-04 16:33:13 STATUS COMPLETED Creating a Corresponding Section in the Report
194 2013-07-04 16:33:13 STATUS COMPLETED Regional Methylation Profiling
195 2013-07-04 16:33:13 STATUS COMPLETED Methylation Profiles
196 2013-07-04 16:33:13 INFO Initialized report index and saved to index.html
197 2013-07-04 16:33:14 STATUS STARTED Differential Methylation - Analysis
198 2013-07-04 16:33:14 INFO Using 0 permutation tests
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
200 2013-07-04 16:33:14 INFO Using region types: tiling,genes,promoters,cpgislands
201 2013-07-04 16:33:14 STATUS STARTED Comparison Information: tumour site
202 2013-07-04 16:33:14 STATUS STARTED Comparing base of tongue-tonsil
203 2013-07-04 16:33:14 STATUS STARTED Computing Differential Methylation Table (Site Level)
204 2013-07-04 16:33:21 INFO Some t-test p-values are NA. They are treated as 1 in FDR adjustment
205 2013-07-04 16:33:28 STATUS COMPLETED Computing Differential Methylation Table (Site Level)
206 2013-07-04 16:33:28 STATUS STARTED Computing Differential Methylation Tables (Region Level)
207 2013-07-04 16:45:21 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
208 2013-07-04 16:45:21 STATUS Computed table for tiling
209 2013-07-04 16:48:07 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
210 2013-07-04 16:48:07 STATUS Computed table for genes
211 2013-07-04 16:50:48 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
212 2013-07-04 16:50:48 STATUS Computed table for promoters
213 2013-07-04 16:53:07 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
214 2013-07-04 16:53:07 STATUS Computed table for cpgislands
215 2013-07-04 16:53:07 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
216 2013-07-04 16:53:07 STATUS COMPLETED Comparing base of tongue-tonsil
217 2013-07-04 16:53:07 STATUS COMPLETED Comparison Information: tumour site
218 2013-07-04 16:53:07 STATUS STARTED Comparison Information: tissue
219 2013-07-04 16:53:07 STATUS STARTED Comparing HPV+ HNSCC tumor-HPV- HNSCC tumor
220 2013-07-04 16:53:07 STATUS STARTED Computing Differential Methylation Table (Site Level)
221 2013-07-04 16:53:12 INFO Some t-test p-values are NA. They are treated as 1 in FDR adjustment
222 2013-07-04 16:53:17 STATUS COMPLETED Computing Differential Methylation Table (Site Level)
223 2013-07-04 16:53:17 STATUS STARTED Computing Differential Methylation Tables (Region Level)
224 2013-07-04 17:04:12 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
225 2013-07-04 17:04:13 STATUS Computed table for tiling
226 2013-07-04 17:06:56 STATUS Computed table for genes
227 2013-07-04 17:09:29 INFO Some p-values are NA. They are treated as 1 in FDR adjustment
228 2013-07-04 17:09:29 STATUS Computed table for promoters
229 2013-07-04 17:11:43 STATUS Computed table for cpgislands
230 2013-07-04 17:11:43 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
231 2013-07-04 17:11:43 STATUS COMPLETED Comparing HPV+ HNSCC tumor-HPV- HNSCC tumor
232 2013-07-04 17:11:43 STATUS COMPLETED Comparison Information: tissue
233 2013-07-04 17:11:43 INFO Skipping enrichment analysis of differentially methylated regions
234 2013-07-04 17:11:43 STATUS COMPLETED Differential Methylation - Analysis
235 2013-07-04 17:11:43 STATUS STARTED Differential Methylation - Report Generation
236 2013-07-04 17:11:43 STATUS Added introductory section
237 2013-07-04 17:11:43 STATUS STARTED Adding Site Level Information
238 2013-07-04 18:03:20 STATUS COMPLETED Adding Site Level Information
239 2013-07-04 18:03:20 STATUS STARTED Adding Region Level Information
240 2013-07-04 18:31:24 STATUS COMPLETED Adding Region Level Information
241 2013-07-04 18:31:24 STATUS COMPLETED Differential Methylation - Report Generation
242 2013-07-04 18:31:25 INFO Initialized report index and saved to index.html
243 2013-07-04 18:31:25 STATUS STARTED Data Export
244 2013-07-04 18:31:25 STATUS STARTED Exporting RnBSet
245 2013-07-04 18:31:25 STATUS STARTED Exporting sites
246 2013-07-04 18:31:25 STATUS STARTED Creating UCSC Track Hub -- bigBed
247 2013-07-04 18:31:25 STATUS STARTED Conversion to BED
248 2013-07-04 18:33:46 STATUS COMPLETED Conversion to BED
249 2013-07-04 18:33:46 STATUS STARTED Creating UCSC Track Hub
250 2013-07-04 18:34:06 STATUS COMPLETED Creating UCSC Track Hub
251 2013-07-04 18:34:06 STATUS COMPLETED Creating UCSC Track Hub -- bigBed
252 2013-07-04 18:34:06 STATUS STARTED Creating UCSC Track Hub -- bigWig
253 2013-07-04 18:34:06 STATUS STARTED Conversion to bedGraph
254 2013-07-04 18:36:10 STATUS COMPLETED Conversion to bedGraph
255 2013-07-04 18:36:10 STATUS STARTED Creating UCSC Track Hub
256 2013-07-04 18:36:28 STATUS COMPLETED Creating UCSC Track Hub
257 2013-07-04 18:36:28 STATUS COMPLETED Creating UCSC Track Hub -- bigWig
258 2013-07-04 18:36:28 STATUS COMPLETED Exporting sites
259 2013-07-04 18:36:28 STATUS COMPLETED Exporting RnBSet
260 2013-07-04 18:36:28 STATUS STARTED Writing export report
261 2013-07-04 18:36:28 STATUS COMPLETED Writing export report
262 2013-07-04 18:36:28 STATUS COMPLETED Data Export
263 2013-07-04 18:36:28 INFO Initialized report index and saved to index.html
264 2013-07-04 18:36:29 STATUS COMPLETED RnBeads Pipeline
265