Harvest for South Atlantic Species List Created 27 Dec 12:05

Harvesting Log

# Logfile created on 2019-12-27 12:05:27 -0500 by logger.rb/56815
[START] [2019-12-27 12:05:27] logged process
[START] [2019-12-27 12:05:27] create_harvest_instance
[STOP] [2019-12-27 12:05:28] create_harvest_instance
[START] [2019-12-27 12:05:28] fetch_files
[STOP] [2019-12-27 12:05:28] fetch_files
[START] [2019-12-27 12:05:28] validate_each_file
[STOP] [2019-12-27 12:05:38] validate_each_file
[START] [2019-12-27 12:05:38] convert_to_csv
[CMD] [2019-12-27 12:05:38] /usr/bin/sort /app/public/converted_csv/s_atlantic_sp_li_refs_19754.csv > /app/public/converted_csv/s_atlantic_sp_li_refs_19754.csv_sorted
[CMD] [2019-12-27 12:05:39] /usr/bin/sort /app/public/converted_csv/s_atlantic_sp_li_nodes_19755.csv > /app/public/converted_csv/s_atlantic_sp_li_nodes_19755.csv_sorted
[CMD] [2019-12-27 12:05:40] /usr/bin/sort /app/public/converted_csv/s_atlantic_sp_li_occurrences_19756.csv > /app/public/converted_csv/s_atlantic_sp_li_occurrences_19756.csv_sorted
[CMD] [2019-12-27 12:05:40] /usr/bin/sort /app/public/converted_csv/s_atlantic_sp_li_measurements_19757.csv > /app/public/converted_csv/s_atlantic_sp_li_measurements_19757.csv_sorted
[STOP] [2019-12-27 12:05:41] convert_to_csv
[START] [2019-12-27 12:05:41] calculate_delta
[CMD] [2019-12-27 12:05:41] echo "0a" > /app/public/diff/s_atlantic_sp_li_refs_19754.diff
[CMD] [2019-12-27 12:05:42] tail -n +1 /app/public/converted_csv/s_atlantic_sp_li_refs_19754.csv >> /app/public/diff/s_atlantic_sp_li_refs_19754.diff
[CMD] [2019-12-27 12:05:42] echo "." >> /app/public/diff/s_atlantic_sp_li_refs_19754.diff
[CMD] [2019-12-27 12:05:43] echo "0a" > /app/public/diff/s_atlantic_sp_li_nodes_19755.diff
[CMD] [2019-12-27 12:05:43] tail -n +1 /app/public/converted_csv/s_atlantic_sp_li_nodes_19755.csv >> /app/public/diff/s_atlantic_sp_li_nodes_19755.diff
[CMD] [2019-12-27 12:05:44] echo "." >> /app/public/diff/s_atlantic_sp_li_nodes_19755.diff
[CMD] [2019-12-27 12:05:45] echo "0a" > /app/public/diff/s_atlantic_sp_li_occurrences_19756.diff
[CMD] [2019-12-27 12:05:45] tail -n +1 /app/public/converted_csv/s_atlantic_sp_li_occurrences_19756.csv >> /app/public/diff/s_atlantic_sp_li_occurrences_19756.diff
[CMD] [2019-12-27 12:05:46] echo "." >> /app/public/diff/s_atlantic_sp_li_occurrences_19756.diff
[CMD] [2019-12-27 12:05:47] echo "0a" > /app/public/diff/s_atlantic_sp_li_measurements_19757.diff
[CMD] [2019-12-27 12:05:47] tail -n +1 /app/public/converted_csv/s_atlantic_sp_li_measurements_19757.csv >> /app/public/diff/s_atlantic_sp_li_measurements_19757.diff
[CMD] [2019-12-27 12:05:48] echo "." >> /app/public/diff/s_atlantic_sp_li_measurements_19757.diff
[STOP] [2019-12-27 12:05:49] calculate_delta
[START] [2019-12-27 12:05:49] parse_diff_and_store
[INFO] [2019-12-27 12:05:49] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-27 12:05:50] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-27 12:06:20] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-27 12:06:29] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-27 12:12:19] Storing 2 References
[INFO] [2019-12-27 12:12:19] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-27 12:12:19] Average Time: 0.0
[INFO] [2019-12-27 12:12:19] Total Time: 1s
[INFO] [2019-12-27 12:12:19] Storing 82655 ScientificNames
[INFO] [2019-12-27 12:12:19] Processing group of 82655 in 83 groups of 1000
[INFO] [2019-12-27 12:12:56] Average Time: 0.433
[INFO] [2019-12-27 12:12:56] Total Time: 37s
[INFO] [2019-12-27 12:12:56] last 3 / first 3: 0.87
[INFO] [2019-12-27 12:12:56] Std.Dev: 0.3082207001484488; Max: 2.86
[INFO] [2019-12-27 12:12:56] Storing 82655 Nodes
[INFO] [2019-12-27 12:12:56] Processing group of 82655 in 83 groups of 1000
[INFO] [2019-12-27 12:13:31] Average Time: 0.419
[INFO] [2019-12-27 12:13:31] Total Time: 36s
[INFO] [2019-12-27 12:13:31] last 3 / first 3: 0.23
[INFO] [2019-12-27 12:13:31] Std.Dev: 0.5244044240850758; Max: 3.46
[INFO] [2019-12-27 12:13:31] Storing 60610 Occurrences
[INFO] [2019-12-27 12:13:31] Processing group of 60610 in 61 groups of 1000
[INFO] [2019-12-27 12:13:38] Average Time: 0.118
[INFO] [2019-12-27 12:13:38] Total Time: 8s
[INFO] [2019-12-27 12:13:38] last 3 / first 3: 1.14
[INFO] [2019-12-27 12:13:38] Std.Dev: 0.03162277660168379; Max: 0.26
[INFO] [2019-12-27 12:13:38] Storing 121220 TraitsReferences
[INFO] [2019-12-27 12:13:38] Processing group of 121220 in 122 groups of 1000
[INFO] [2019-12-27 12:13:54] Average Time: 0.124
[INFO] [2019-12-27 12:13:54] Total Time: 16s
[INFO] [2019-12-27 12:13:54] last 3 / first 3: 0.48
[INFO] [2019-12-27 12:13:54] Std.Dev: 0.3478505426185217; Max: 3.43
[INFO] [2019-12-27 12:13:54] Storing 121220 Traits
[INFO] [2019-12-27 12:13:54] Processing group of 121220 in 122 groups of 1000
[INFO] [2019-12-27 12:14:43] Average Time: 0.4
[INFO] [2019-12-27 12:14:43] Total Time: 50s
[INFO] [2019-12-27 12:14:43] last 3 / first 3: 0.62
[INFO] [2019-12-27 12:14:43] Std.Dev: 0.5531726674375732; Max: 3.98
[INFO] [2019-12-27 12:14:43] Storing 121092 MetaTraits
[INFO] [2019-12-27 12:14:43] Processing group of 121092 in 122 groups of 1000
[INFO] [2019-12-27 12:15:14] Average Time: 0.25
[INFO] [2019-12-27 12:15:14] Total Time: 31s
[INFO] [2019-12-27 12:15:14] last 3 / first 3: 0.68
[INFO] [2019-12-27 12:15:14] Std.Dev: 0.7106335201775947; Max: 4.23
[STOP] [2019-12-27 12:15:14] parse_diff_and_store
[START] [2019-12-27 12:15:14] resolve_keys
[INFO] [2019-12-27 12:17:54] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-27 12:18:04] traits to occurrences...
[INFO] [2019-12-27 12:18:13] traits to nodes (through occurrences)...
[INFO] [2019-12-27 12:18:15] Traits to sex term...
[INFO] [2019-12-27 12:18:22] Traits to lifestage term...
[INFO] [2019-12-27 12:18:29] MetaTraits to traits...
[INFO] [2019-12-27 12:18:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-27 12:18:52] Assocs to occurrences...
[INFO] [2019-12-27 12:18:52] Assocs to nodes...
[INFO] [2019-12-27 12:18:52] Assoc to sex term...
[INFO] [2019-12-27 12:18:52] Assoc to lifestage term...
[STOP] [2019-12-27 12:18:52] resolve_keys
[START] [2019-12-27 12:18:52] hold_for_later_1
[STOP] [2019-12-27 12:18:52] hold_for_later_1
[START] [2019-12-27 12:18:52] hold_for_later_2
[STOP] [2019-12-27 12:18:52] hold_for_later_2
[START] [2019-12-27 12:18:52] resolve_missing_parents
[STOP] [2019-12-27 12:20:37] resolve_missing_parents
[START] [2019-12-27 12:20:37] rebuild_nodes
[START] [2019-12-27 12:20:37] Flattener#flatten
[START] [2019-12-27 12:20:37] Flattener#study_resource
[START] [2019-12-27 12:20:37] Flattener#build_ancestry
[STOP] [2019-12-27 12:20:55] Flattener#build_ancestry
[INFO] [2019-12-27 12:20:55] 82655 ancestry keys
[START] [2019-12-27 12:20:55] build_node_ancestors
[INFO] [2019-12-27 12:20:55] old ancestors deleted.
[STOP] [2019-12-27 12:21:58] build_node_ancestors
[START] [2019-12-27 12:22:03] Flattener#propagate_ancestor_ids
[STOP] [2019-12-27 12:22:16] Flattener#propagate_ancestor_ids
[STOP] [2019-12-27 12:22:16] Flattener#flatten
[STOP] [2019-12-27 12:22:16] rebuild_nodes
[START] [2019-12-27 12:22:16] resolve_missing_media_owners
[STOP] [2019-12-27 12:22:16] resolve_missing_media_owners
[START] [2019-12-27 12:22:16] sanitize_media_verbatims
[STOP] [2019-12-27 12:22:16] sanitize_media_verbatims
[START] [2019-12-27 12:22:16] queue_downloads
[STOP] [2019-12-27 12:22:16] queue_downloads
[START] [2019-12-27 12:22:16] parse_names
[WARN] [2019-12-27 12:22:16] I see 82655 names which still need to be parsed.
[STOP] [2019-12-27 12:23:20] parse_names
[START] [2019-12-27 12:23:20] denormalize_canonical_names_to_nodes
[STOP] [2019-12-27 12:23:21] denormalize_canonical_names_to_nodes
[START] [2019-12-27 12:23:21] match_nodes
[START] [2019-12-27 12:23:21] map_all_nodes_to_pages
[STOP] [2019-12-27 16:19:39] map_all_nodes_to_pages
[INFO] [2019-12-27 16:19:39] 4936 Unmatched nodes (of 82655)! That's too many to output. First 10: Diplodus rondeleti (#62612849); Pagellus bellotti (#62635601); Virididentex multidens (#62607531); Trachinotus glaucus (#62591736); Carangoides armata (#62606579); Eques (#62613992); Gobionellus lanceolatus (#62599849); Trematomus dubia (#62613738); Paranotothenia macrocephala (#62593697); Kajikia albidus (#62567335)
[START] [2019-12-27 16:19:39] update_nodes
[STOP] [2019-12-27 16:20:10] update_nodes
[STOP] [2019-12-27 16:20:10] match_nodes
[START] [2019-12-27 16:20:10] reindex_search
[STOP] [2019-12-27 16:23:48] reindex_search
[START] [2019-12-27 16:23:48] normalize_units
[STOP] [2019-12-27 16:23:48] normalize_units
[START] [2019-12-27 16:23:48] calculate_statistics
[STOP] [2019-12-27 16:23:49] calculate_statistics
[START] [2019-12-27 16:23:49] complete_harvest_instance
[START] [2019-12-27 16:23:49] overall_tsv_creation
[INFO] [2019-12-27 16:23:49] Processing group of 82655 in 9 batches of 10000
[INFO] [2019-12-27 16:25:31] 5383 Traits (unfiltered)...
[INFO] [2019-12-27 16:25:44] 5383 Traits (filtered)...
[INFO] [2019-12-27 16:25:44] 0 Associations (filtered)...
[INFO] [2019-12-27 16:26:32] 26908 metadata added.
[INFO] [2019-12-27 16:26:32] 0 metadata added.
[INFO] [2019-12-27 16:28:08] 6595 Traits (unfiltered)...
[INFO] [2019-12-27 16:28:21] 6595 Traits (filtered)...
[INFO] [2019-12-27 16:28:21] 0 Associations (filtered)...
[INFO] [2019-12-27 16:29:12] 32966 metadata added.
[INFO] [2019-12-27 16:29:12] 0 metadata added.
[INFO] [2019-12-27 16:30:48] 7173 Traits (unfiltered)...
[INFO] [2019-12-27 16:31:01] 7173 Traits (filtered)...
[INFO] [2019-12-27 16:31:01] 0 Associations (filtered)...
[INFO] [2019-12-27 16:31:57] 35856 metadata added.
[INFO] [2019-12-27 16:31:57] 0 metadata added.
[INFO] [2019-12-27 16:33:33] 7532 Traits (unfiltered)...
[INFO] [2019-12-27 16:33:46] 7532 Traits (filtered)...
[INFO] [2019-12-27 16:33:46] 0 Associations (filtered)...
[INFO] [2019-12-27 16:34:41] 37652 metadata added.
[INFO] [2019-12-27 16:34:41] 0 metadata added.
[INFO] [2019-12-27 16:36:14] 7685 Traits (unfiltered)...
[INFO] [2019-12-27 16:36:28] 7685 Traits (filtered)...
[INFO] [2019-12-27 16:36:28] 0 Associations (filtered)...
[INFO] [2019-12-27 16:37:22] 38413 metadata added.
[INFO] [2019-12-27 16:37:22] 0 metadata added.
[INFO] [2019-12-27 16:38:56] 7714 Traits (unfiltered)...
[INFO] [2019-12-27 16:39:09] 7714 Traits (filtered)...
[INFO] [2019-12-27 16:39:09] 0 Associations (filtered)...
[INFO] [2019-12-27 16:40:04] 38551 metadata added.
[INFO] [2019-12-27 16:40:04] 0 metadata added.
[INFO] [2019-12-27 16:41:38] 7963 Traits (unfiltered)...
[INFO] [2019-12-27 16:41:51] 7963 Traits (filtered)...
[INFO] [2019-12-27 16:41:52] 0 Associations (filtered)...
[INFO] [2019-12-27 16:42:47] 39785 metadata added.
[INFO] [2019-12-27 16:42:47] 0 metadata added.
[INFO] [2019-12-27 16:44:21] 8329 Traits (unfiltered)...
[INFO] [2019-12-27 16:44:34] 8329 Traits (filtered)...
[INFO] [2019-12-27 16:44:34] 0 Associations (filtered)...
[INFO] [2019-12-27 16:45:30] 41616 metadata added.
[INFO] [2019-12-27 16:45:30] 0 metadata added.
[INFO] [2019-12-27 16:46:29] 2236 Traits (unfiltered)...
[INFO] [2019-12-27 16:46:42] 2236 Traits (filtered)...
[INFO] [2019-12-27 16:46:42] 0 Associations (filtered)...
[INFO] [2019-12-27 16:47:23] 11175 metadata added.
[INFO] [2019-12-27 16:47:23] 0 metadata added.
[INFO] [2019-12-27 16:47:23] Average Time: 127.157
[INFO] [2019-12-27 16:47:23] Total Time: 23m35s
[INFO] [2019-12-27 16:47:23] last 3 / first 3: 0.94
[INFO] [2019-12-27 16:47:23] Std.Dev: 14.625901681605821; Max: 135.53
[STOP] [2019-12-27 16:47:23] overall_tsv_creation
[INFO] [2019-12-27 16:47:23] Done. Check your files:
[INFO] [2019-12-27 16:47:24] (82655 lines) /app/public/data/s_atlantic_sp_li/publish_nodes.tsv
[INFO] [2019-12-27 16:47:24] (460848 lines) /app/public/data/s_atlantic_sp_li/publish_node_ancestors.tsv
[INFO] [2019-12-27 16:47:25] (82655 lines) /app/public/data/s_atlantic_sp_li/publish_scientific_names.tsv
[INFO] [2019-12-27 16:47:26] (60611 lines) /app/public/data/s_atlantic_sp_li/publish_traits.tsv
[INFO] [2019-12-27 16:47:26] (302923 lines) /app/public/data/s_atlantic_sp_li/publish_metadata.tsv
[STOP] [2019-12-27 16:47:26] complete_harvest_instance
[START] [2019-12-27 16:47:26] completed
[STOP] [2019-12-27 16:47:26] completed
[STOP] [2019-12-27 16:47:26] logged process, took 16919.46

Latest Process

27 Dec 12:05 EXITED currently processing 0