Harvest for NCBI GGBN GBIF BHL BOLDS data coverage Created 23 Dec 08:53

Stage: completed
Fetched: 23 Dec 08:53
Validated: 23 Dec 08:53
Deltas Created 23 Dec 08:53
Units Normalized: 23 Dec 09:04
Ancestry Built: 23 Dec 08:55
Nodes Matched: 23 Dec 09:04
Names Parsed: 23 Dec 08:55
New Models Stored: 23 Dec 08:55
Indexed: 23 Dec 09:04
Completed: 23 Dec 09:14
Time to Harvest: less than a minute

Harvesting Log

(132 lines)
# Logfile created on 2020-12-23 08:52:17 -0500 by logger.rb/v1.4.2
[INFO] [2020-12-23 08:52:17] ## HARVEST: type = re_-harvest
[START] [2020-12-23 08:53:28] logged process: ca5be136aef877c71c74100a42de34a9e7a07645

[START] [2020-12-23 08:53:28] create_harvest_instance
[STOP] [2020-12-23 08:53:29] create_harvest_instance
[START] [2020-12-23 08:53:29] fetch_files
[STOP] [2020-12-23 08:53:29] fetch_files
[START] [2020-12-23 08:53:29] validate_each_file
[STOP] [2020-12-23 08:53:34] validate_each_file
[START] [2020-12-23 08:53:34] convert_to_csv
[CMD] [2020-12-23 08:53:34] /usr/bin/sort /app/public/converted_csv/nnnnndc_nodes_25716.csv > /app/public/converted_csv/nnnnndc_nodes_25716.csv_sorted
[CMD] [2020-12-23 08:53:34] /usr/bin/sort /app/public/converted_csv/nnnnndc_occurrences_25717.csv > /app/public/converted_csv/nnnnndc_occurrences_25717.csv_sorted
[CMD] [2020-12-23 08:53:34] /usr/bin/sort /app/public/converted_csv/nnnnndc_measurements_25718.csv > /app/public/converted_csv/nnnnndc_measurements_25718.csv_sorted
[STOP] [2020-12-23 08:53:34] convert_to_csv
[START] [2020-12-23 08:53:34] calculate_delta
[CMD] [2020-12-23 08:53:34] echo "0a" > /app/public/diff/nnnnndc_nodes_25716.diff
[CMD] [2020-12-23 08:53:34] tail -n +1 /app/public/converted_csv/nnnnndc_nodes_25716.csv >> /app/public/diff/nnnnndc_nodes_25716.diff
[CMD] [2020-12-23 08:53:35] echo "." >> /app/public/diff/nnnnndc_nodes_25716.diff
[CMD] [2020-12-23 08:53:35] echo "0a" > /app/public/diff/nnnnndc_occurrences_25717.diff
[CMD] [2020-12-23 08:53:35] tail -n +1 /app/public/converted_csv/nnnnndc_occurrences_25717.csv >> /app/public/diff/nnnnndc_occurrences_25717.diff
[CMD] [2020-12-23 08:53:35] echo "." >> /app/public/diff/nnnnndc_occurrences_25717.diff
[CMD] [2020-12-23 08:53:35] echo "0a" > /app/public/diff/nnnnndc_measurements_25718.diff
[CMD] [2020-12-23 08:53:35] tail -n +1 /app/public/converted_csv/nnnnndc_measurements_25718.csv >> /app/public/diff/nnnnndc_measurements_25718.diff
[CMD] [2020-12-23 08:53:35] echo "." >> /app/public/diff/nnnnndc_measurements_25718.diff
[STOP] [2020-12-23 08:53:35] calculate_delta
[START] [2020-12-23 08:53:35] parse_diff_and_store
[INFO] [2020-12-23 08:53:35] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-23 08:53:37] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-23 08:53:49] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-23 08:54:16] Storing 9917 ScientificNames
[INFO] [2020-12-23 08:54:16] Processing group of 9917 in 10 groups of 1000
[INFO] [2020-12-23 08:54:19] Average Time: 0.289
[INFO] [2020-12-23 08:54:19] Total Time: 3s
[INFO] [2020-12-23 08:54:19] last 3 / first 3: 1.06
[INFO] [2020-12-23 08:54:19] Std.Dev: 0.0; Max: 0.33
[INFO] [2020-12-23 08:54:19] Storing 9917 Nodes
[INFO] [2020-12-23 08:54:19] Processing group of 9917 in 10 groups of 1000
[INFO] [2020-12-23 08:54:21] Average Time: 0.241
[INFO] [2020-12-23 08:54:21] Total Time: 3s
[INFO] [2020-12-23 08:54:21] last 3 / first 3: 0.88
[INFO] [2020-12-23 08:54:21] Std.Dev: 0.0; Max: 0.3
[INFO] [2020-12-23 08:54:21] Storing 116360 Occurrences
[INFO] [2020-12-23 08:54:21] Processing group of 116360 in 117 groups of 1000
[INFO] [2020-12-23 08:54:36] Average Time: 0.122
[INFO] [2020-12-23 08:54:36] Total Time: 15s
[INFO] [2020-12-23 08:54:36] last 3 / first 3: 0.74
[INFO] [2020-12-23 08:54:36] Std.Dev: 0.08944271909999159; Max: 1.02
[INFO] [2020-12-23 08:54:36] Storing 116456 Traits
[INFO] [2020-12-23 08:54:36] Processing group of 116456 in 117 groups of 1000
[INFO] [2020-12-23 08:55:19] Average Time: 0.357
[INFO] [2020-12-23 08:55:19] Total Time: 43s
[INFO] [2020-12-23 08:55:19] last 3 / first 3: 0.65
[INFO] [2020-12-23 08:55:19] Std.Dev: 0.22135943621178655; Max: 1.93
[STOP] [2020-12-23 08:55:19] parse_diff_and_store
[START] [2020-12-23 08:55:19] resolve_keys
[INFO] [2020-12-23 08:55:34] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-23 08:55:36] traits to occurrences...
[INFO] [2020-12-23 08:55:42] traits to nodes (through occurrences)...
[INFO] [2020-12-23 08:55:44] Traits to sex term...
[INFO] [2020-12-23 08:55:46] Traits to lifestage term...
[INFO] [2020-12-23 08:55:48] MetaTraits to traits...
[INFO] [2020-12-23 08:55:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-23 08:55:48] Assocs to occurrences...
[INFO] [2020-12-23 08:55:48] Assocs to nodes...
[INFO] [2020-12-23 08:55:48] Assoc to sex term...
[INFO] [2020-12-23 08:55:48] Assoc to lifestage term...
[INFO] [2020-12-23 08:55:48] MetaAssoc to assocs...
[STOP] [2020-12-23 08:55:48] resolve_keys
[START] [2020-12-23 08:55:48] hold_for_later_1
[STOP] [2020-12-23 08:55:48] hold_for_later_1
[START] [2020-12-23 08:55:48] hold_for_later_2
[STOP] [2020-12-23 08:55:48] hold_for_later_2
[START] [2020-12-23 08:55:48] resolve_missing_parents
[STOP] [2020-12-23 08:55:48] resolve_missing_parents
[START] [2020-12-23 08:55:48] rebuild_nodes
[START] [2020-12-23 08:55:48] Flattener#flatten
[START] [2020-12-23 08:55:48] Flattener#study_resource
[START] [2020-12-23 08:55:48] Flattener#build_ancestry
[STOP] [2020-12-23 08:55:49] Flattener#build_ancestry
[INFO] [2020-12-23 08:55:49] 9917 ancestry keys
[START] [2020-12-23 08:55:49] build_node_ancestors
[INFO] [2020-12-23 08:55:49] old ancestors deleted.
[STOP] [2020-12-23 08:55:49] build_node_ancestors
[WARN] [2020-12-23 08:55:49] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-23 08:55:49] Flattener#flatten
[STOP] [2020-12-23 08:55:49] rebuild_nodes
[START] [2020-12-23 08:55:49] resolve_missing_media_owners
[STOP] [2020-12-23 08:55:49] resolve_missing_media_owners
[START] [2020-12-23 08:55:49] sanitize_media_verbatims
[STOP] [2020-12-23 08:55:49] sanitize_media_verbatims
[START] [2020-12-23 08:55:49] queue_downloads
[STOP] [2020-12-23 08:55:49] queue_downloads
[START] [2020-12-23 08:55:49] parse_names
[WARN] [2020-12-23 08:55:49] I see 9917 names which still need to be parsed.
[STOP] [2020-12-23 08:55:58] parse_names
[START] [2020-12-23 08:55:58] denormalize_canonical_names_to_nodes
[STOP] [2020-12-23 08:55:58] denormalize_canonical_names_to_nodes
[START] [2020-12-23 08:55:58] match_nodes
[START] [2020-12-23 08:55:58] map_all_nodes_to_pages
[STOP] [2020-12-23 09:04:12] map_all_nodes_to_pages
[INFO] [2020-12-23 09:04:12] 1089 Unmatched nodes (of 9917)! That's too many to output. Full list in /app/public/data/nnnnndc/unmatched_nodes.txt ; First 10: Abacioninae (#87362240); Ablechroiulidae (#87362242); Ablechroiulinae (#87362243); Abrsidae (#87362245); Acanthamoebidae (#87362255); Acanthephyridae (#87362258); Acanthocollidae (#87362268); Acanthoeccidae (#87362273); Acanthoperlidae (#87362279); Achilixiinae (#87362309)
[START] [2020-12-23 09:04:12] update_nodes
[STOP] [2020-12-23 09:04:16] update_nodes
[STOP] [2020-12-23 09:04:16] match_nodes
[START] [2020-12-23 09:04:16] reindex_search
[STOP] [2020-12-23 09:04:23] reindex_search
[START] [2020-12-23 09:04:23] normalize_units
[STOP] [2020-12-23 09:04:24] normalize_units
[START] [2020-12-23 09:04:24] calculate_statistics
[2020-12-23 09:04:24] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-23 09:04:24] calculate_statistics
[START] [2020-12-23 09:04:24] complete_harvest_instance
[START] [2020-12-23 09:04:24] overall_tsv_creation
[INFO] [2020-12-23 09:04:24] Processing group of 9917 in 1 batches of 10000
[INFO] [2020-12-23 09:05:30] 116432 Traits (unfiltered)...
[INFO] [2020-12-23 09:13:23] 116432 Traits (filtered)...
[INFO] [2020-12-23 09:13:26] 0 Associations (filtered)...
[INFO] [2020-12-23 09:13:34] 0 metadata added.
[INFO] [2020-12-23 09:13:34] 0 metadata added.
[INFO] [2020-12-23 09:14:20] Average Time: 566.57
[INFO] [2020-12-23 09:14:20] Total Time: 9m56s
[STOP] [2020-12-23 09:14:20] overall_tsv_creation
[INFO] [2020-12-23 09:14:20] Done. Check your files:
[INFO] [2020-12-23 09:14:20] (9917 lines) /app/public/data/nnnnndc/publish_nodes.tsv
[INFO] [2020-12-23 09:14:20] (9917 lines) /app/public/data/nnnnndc/publish_scientific_names.tsv
[INFO] [2020-12-23 09:14:20] (116433 lines) /app/public/data/nnnnndc/publish_traits.tsv
[INFO] [2020-12-23 09:14:20] (1 lines) /app/public/data/nnnnndc/publish_metadata.tsv
[STOP] [2020-12-23 09:14:20] complete_harvest_instance
[START] [2020-12-23 09:14:20] completed
[STOP] [2020-12-23 09:14:20] completed
[STOP] [2020-12-23 09:14:20] logged process, took 1252.09

Latest Process