Harvest for Gulf of Guinea Species List Created 23 Dec 08:15

Stage: completed
Fetched: 23 Dec 08:15
Validated: 23 Dec 08:15
Deltas Created 23 Dec 08:15
Units Normalized: 23 Dec 09:13
Ancestry Built: 23 Dec 08:19
Nodes Matched: 23 Dec 09:12
Names Parsed: 23 Dec 08:19
New Models Stored: 23 Dec 08:17
Indexed: 23 Dec 09:13
Completed: 23 Dec 09:18
Time to Harvest: 1 minute
Harvesting Log

(156 lines)
# Logfile created on 2019-12-23 08:15:37 -0500 by logger.rb/56815
[START] [2019-12-23 08:15:37] logged process
[START] [2019-12-23 08:15:37] create_harvest_instance
[STOP] [2019-12-23 08:15:37] create_harvest_instance
[START] [2019-12-23 08:15:37] fetch_files
[STOP] [2019-12-23 08:15:37] fetch_files
[START] [2019-12-23 08:15:37] validate_each_file
[STOP] [2019-12-23 08:15:40] validate_each_file
[START] [2019-12-23 08:15:40] convert_to_csv
[CMD] [2019-12-23 08:15:40] /usr/bin/sort /app/public/converted_csv/gulf_guinea_sp_l_refs_19314.csv > /app/public/converted_csv/gulf_guinea_sp_l_refs_19314.csv_sorted
[CMD] [2019-12-23 08:15:40] /usr/bin/sort /app/public/converted_csv/gulf_guinea_sp_l_nodes_19315.csv > /app/public/converted_csv/gulf_guinea_sp_l_nodes_19315.csv_sorted
[CMD] [2019-12-23 08:15:41] /usr/bin/sort /app/public/converted_csv/gulf_guinea_sp_l_occurrences_19316.csv > /app/public/converted_csv/gulf_guinea_sp_l_occurrences_19316.csv_sorted
[CMD] [2019-12-23 08:15:42] /usr/bin/sort /app/public/converted_csv/gulf_guinea_sp_l_measurements_19317.csv > /app/public/converted_csv/gulf_guinea_sp_l_measurements_19317.csv_sorted
[STOP] [2019-12-23 08:15:42] convert_to_csv
[START] [2019-12-23 08:15:42] calculate_delta
[CMD] [2019-12-23 08:15:42] echo "0a" > /app/public/diff/gulf_guinea_sp_l_refs_19314.diff
[CMD] [2019-12-23 08:15:43] tail -n +1 /app/public/converted_csv/gulf_guinea_sp_l_refs_19314.csv >> /app/public/diff/gulf_guinea_sp_l_refs_19314.diff
[CMD] [2019-12-23 08:15:44] echo "." >> /app/public/diff/gulf_guinea_sp_l_refs_19314.diff
[CMD] [2019-12-23 08:15:44] echo "0a" > /app/public/diff/gulf_guinea_sp_l_nodes_19315.diff
[CMD] [2019-12-23 08:15:45] tail -n +1 /app/public/converted_csv/gulf_guinea_sp_l_nodes_19315.csv >> /app/public/diff/gulf_guinea_sp_l_nodes_19315.diff
[CMD] [2019-12-23 08:15:46] echo "." >> /app/public/diff/gulf_guinea_sp_l_nodes_19315.diff
[CMD] [2019-12-23 08:15:46] echo "0a" > /app/public/diff/gulf_guinea_sp_l_occurrences_19316.diff
[CMD] [2019-12-23 08:15:47] tail -n +1 /app/public/converted_csv/gulf_guinea_sp_l_occurrences_19316.csv >> /app/public/diff/gulf_guinea_sp_l_occurrences_19316.diff
[CMD] [2019-12-23 08:15:48] echo "." >> /app/public/diff/gulf_guinea_sp_l_occurrences_19316.diff
[CMD] [2019-12-23 08:15:48] echo "0a" > /app/public/diff/gulf_guinea_sp_l_measurements_19317.diff
[CMD] [2019-12-23 08:15:49] tail -n +1 /app/public/converted_csv/gulf_guinea_sp_l_measurements_19317.csv >> /app/public/diff/gulf_guinea_sp_l_measurements_19317.diff
[CMD] [2019-12-23 08:15:50] echo "." >> /app/public/diff/gulf_guinea_sp_l_measurements_19317.diff
[STOP] [2019-12-23 08:15:50] calculate_delta
[START] [2019-12-23 08:15:50] parse_diff_and_store
[INFO] [2019-12-23 08:15:51] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 08:15:52] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 08:15:58] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 08:16:00] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 08:16:50] Storing 2 References
[INFO] [2019-12-23 08:16:50] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 08:16:50] Average Time: 0.0
[INFO] [2019-12-23 08:16:50] Total Time: 1s
[INFO] [2019-12-23 08:16:50] Storing 14202 ScientificNames
[INFO] [2019-12-23 08:16:50] Processing group of 14202 in 15 groups of 1000
[INFO] [2019-12-23 08:16:56] Average Time: 0.37
[INFO] [2019-12-23 08:16:56] Total Time: 6s
[INFO] [2019-12-23 08:16:56] last 3 / first 3: 0.68
[INFO] [2019-12-23 08:16:56] Std.Dev: 0.08944271909999159; Max: 0.5
[INFO] [2019-12-23 08:16:56] Storing 14202 Nodes
[INFO] [2019-12-23 08:16:56] Processing group of 14202 in 15 groups of 1000
[INFO] [2019-12-23 08:17:01] Average Time: 0.347
[INFO] [2019-12-23 08:17:01] Total Time: 6s
[INFO] [2019-12-23 08:17:01] last 3 / first 3: 0.68
[INFO] [2019-12-23 08:17:01] Std.Dev: 0.15811388300841897; Max: 0.85
[INFO] [2019-12-23 08:17:01] Storing 8736 Occurrences
[INFO] [2019-12-23 08:17:01] Processing group of 8736 in 9 groups of 1000
[INFO] [2019-12-23 08:17:02] Average Time: 0.117
[INFO] [2019-12-23 08:17:02] Total Time: 2s
[INFO] [2019-12-23 08:17:02] last 3 / first 3: 1.0
[INFO] [2019-12-23 08:17:02] Std.Dev: 0.0; Max: 0.16
[INFO] [2019-12-23 08:17:02] Storing 17472 TraitsReferences
[INFO] [2019-12-23 08:17:02] Processing group of 17472 in 18 groups of 1000
[INFO] [2019-12-23 08:17:04] Average Time: 0.077
[INFO] [2019-12-23 08:17:04] Total Time: 2s
[INFO] [2019-12-23 08:17:04] last 3 / first 3: 0.59
[INFO] [2019-12-23 08:17:04] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-12-23 08:17:04] Storing 17472 Traits
[INFO] [2019-12-23 08:17:04] Processing group of 17472 in 18 groups of 1000
[INFO] [2019-12-23 08:17:10] Average Time: 0.323
[INFO] [2019-12-23 08:17:10] Total Time: 6s
[INFO] [2019-12-23 08:17:10] last 3 / first 3: 0.72
[INFO] [2019-12-23 08:17:10] Std.Dev: 0.06324555320336758; Max: 0.5
[INFO] [2019-12-23 08:17:10] Storing 17464 MetaTraits
[INFO] [2019-12-23 08:17:10] Processing group of 17464 in 18 groups of 1000
[INFO] [2019-12-23 08:17:12] Average Time: 0.133
[INFO] [2019-12-23 08:17:12] Total Time: 3s
[INFO] [2019-12-23 08:17:12] last 3 / first 3: 0.86
[INFO] [2019-12-23 08:17:12] Std.Dev: 0.03162277660168379; Max: 0.18
[STOP] [2019-12-23 08:17:12] parse_diff_and_store
[START] [2019-12-23 08:17:12] resolve_keys
[INFO] [2019-12-23 08:18:05] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 08:18:09] traits to occurrences...
[INFO] [2019-12-23 08:18:15] traits to nodes (through occurrences)...
[INFO] [2019-12-23 08:18:15] Traits to sex term...
[INFO] [2019-12-23 08:18:20] Traits to lifestage term...
[INFO] [2019-12-23 08:18:25] MetaTraits to traits...
[INFO] [2019-12-23 08:18:26] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 08:18:29] Assocs to occurrences...
[INFO] [2019-12-23 08:18:29] Assocs to nodes...
[INFO] [2019-12-23 08:18:29] Assoc to sex term...
[INFO] [2019-12-23 08:18:29] Assoc to lifestage term...
[STOP] [2019-12-23 08:18:29] resolve_keys
[START] [2019-12-23 08:18:29] hold_for_later_1
[STOP] [2019-12-23 08:18:29] hold_for_later_1
[START] [2019-12-23 08:18:29] hold_for_later_2
[STOP] [2019-12-23 08:18:29] hold_for_later_2
[START] [2019-12-23 08:18:29] resolve_missing_parents
[STOP] [2019-12-23 08:18:55] resolve_missing_parents
[START] [2019-12-23 08:18:55] rebuild_nodes
[START] [2019-12-23 08:18:55] Flattener#flatten
[START] [2019-12-23 08:18:55] Flattener#study_resource
[START] [2019-12-23 08:18:55] Flattener#build_ancestry
[STOP] [2019-12-23 08:18:56] Flattener#build_ancestry
[INFO] [2019-12-23 08:18:56] 14202 ancestry keys
[START] [2019-12-23 08:18:56] build_node_ancestors
[INFO] [2019-12-23 08:18:56] old ancestors deleted.
[STOP] [2019-12-23 08:19:02] build_node_ancestors
[START] [2019-12-23 08:19:09] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 08:19:11] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 08:19:11] Flattener#flatten
[STOP] [2019-12-23 08:19:11] rebuild_nodes
[START] [2019-12-23 08:19:11] resolve_missing_media_owners
[STOP] [2019-12-23 08:19:11] resolve_missing_media_owners
[START] [2019-12-23 08:19:11] sanitize_media_verbatims
[STOP] [2019-12-23 08:19:11] sanitize_media_verbatims
[START] [2019-12-23 08:19:11] queue_downloads
[STOP] [2019-12-23 08:19:11] queue_downloads
[START] [2019-12-23 08:19:11] parse_names
[WARN] [2019-12-23 08:19:11] I see 14202 names which still need to be parsed.
[STOP] [2019-12-23 08:19:23] parse_names
[START] [2019-12-23 08:19:23] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 08:19:23] denormalize_canonical_names_to_nodes
[START] [2019-12-23 08:19:23] match_nodes
[START] [2019-12-23 08:19:23] map_all_nodes_to_pages
[STOP] [2019-12-23 09:12:41] map_all_nodes_to_pages
[INFO] [2019-12-23 09:12:41] 974 Unmatched nodes (of 14202)! That's too many to output. First 10: Pagellus bellotti (#61925463); Epinephelus esonue (#61929551); Serranus africana (#61926721); Apogon stauchi (#61927030); Porogobius schlegeli (#61927252); Centracanthidae (#61918823); Scorpaeniformes (#61918162); Trigloporus (#61918517); Pellonula normani (#61926614); Trachinocephalus (#61918803)
[START] [2019-12-23 09:12:41] update_nodes
[STOP] [2019-12-23 09:12:46] update_nodes
[STOP] [2019-12-23 09:12:46] match_nodes
[START] [2019-12-23 09:12:46] reindex_search
[STOP] [2019-12-23 09:13:36] reindex_search
[START] [2019-12-23 09:13:36] normalize_units
[STOP] [2019-12-23 09:13:36] normalize_units
[START] [2019-12-23 09:13:36] calculate_statistics
[STOP] [2019-12-23 09:13:36] calculate_statistics
[START] [2019-12-23 09:13:36] complete_harvest_instance
[START] [2019-12-23 09:13:36] overall_tsv_creation
[INFO] [2019-12-23 09:13:36] Processing group of 14202 in 2 batches of 10000
[INFO] [2019-12-23 09:15:08] 5760 Traits (unfiltered)...
[INFO] [2019-12-23 09:15:22] 5760 Traits (filtered)...
[INFO] [2019-12-23 09:15:22] 0 Associations (filtered)...
[INFO] [2019-12-23 09:16:12] 28793 metadata added.
[INFO] [2019-12-23 09:16:12] 0 metadata added.
[INFO] [2019-12-23 09:17:19] 2976 Traits (unfiltered)...
[INFO] [2019-12-23 09:17:32] 2976 Traits (filtered)...
[INFO] [2019-12-23 09:17:32] 0 Associations (filtered)...
[INFO] [2019-12-23 09:18:14] 14879 metadata added.
[INFO] [2019-12-23 09:18:14] 0 metadata added.
[INFO] [2019-12-23 09:18:14] Average Time: 111.64
[INFO] [2019-12-23 09:18:14] Total Time: 4m39s
[STOP] [2019-12-23 09:18:14] overall_tsv_creation
[INFO] [2019-12-23 09:18:14] Done. Check your files:
[INFO] [2019-12-23 09:18:15] (14202 lines) /app/public/data/gulf_guinea_sp_l/publish_nodes.tsv
[INFO] [2019-12-23 09:18:16] (75470 lines) /app/public/data/gulf_guinea_sp_l/publish_node_ancestors.tsv
[INFO] [2019-12-23 09:18:16] (14202 lines) /app/public/data/gulf_guinea_sp_l/publish_scientific_names.tsv
[INFO] [2019-12-23 09:18:17] (8737 lines) /app/public/data/gulf_guinea_sp_l/publish_traits.tsv
[INFO] [2019-12-23 09:18:18] (43673 lines) /app/public/data/gulf_guinea_sp_l/publish_metadata.tsv
[STOP] [2019-12-23 09:18:18] complete_harvest_instance
[START] [2019-12-23 09:18:18] completed
[STOP] [2019-12-23 09:18:18] completed
[STOP] [2019-12-23 09:18:18] logged process, took 3761.14
Latest Process

23 Dec 08:15 EXITED currently processing 0