Harvest for GBIF national node type records Germany Created 11 Jun 11:29

Harvesting Log

[INFO] [2021-06-11 11:29:34] Created harvest instance #4029
[STOP] [2021-06-11 11:29:34] create_harvest_instance
[START] [2021-06-11 11:29:34] fetch_files
[STOP] [2021-06-11 11:29:34] fetch_files
[START] [2021-06-11 11:29:34] validate_each_file
[INFO] [2021-06-11 11:29:34] Looping over 3 formats...
[INFO] [2021-06-11 11:29:34] ...nodes (/app/public/data/gnntrg/taxon.tab)
[INFO] [2021-06-11 11:29:41] Valid: /app/public/converted_csv/gnntrg_nodes_4029.csv (140395 lines)
[INFO] [2021-06-11 11:29:41] ...occurrences (/app/public/data/gnntrg/occurrence.tab)
[INFO] [2021-06-11 11:29:55] Valid: /app/public/converted_csv/gnntrg_occurrences_4029.csv (279289 lines)
[INFO] [2021-06-11 11:29:55] ...measurements (/app/public/data/gnntrg/measurement_or_fact.tab)
[INFO] [2021-06-11 11:31:06] Valid: /app/public/converted_csv/gnntrg_measurements_4029.csv (1910814 lines)
[STOP] [2021-06-11 11:31:06] validate_each_file
[START] [2021-06-11 11:31:06] convert_to_csv
[INFO] [2021-06-11 11:31:06] Looping over 3 formats...
[INFO] [2021-06-11 11:31:06] ...nodes (/app/public/data/gnntrg/taxon.tab)
[CMD] [2021-06-11 11:31:06] /usr/bin/sort /app/public/converted_csv/gnntrg_nodes_4029.csv > /app/public/converted_csv/gnntrg_nodes_4029.csv_sorted
[INFO] [2021-06-11 11:31:06] Converted: /app/public/converted_csv/gnntrg_nodes_4029.csv (140395 lines)
[INFO] [2021-06-11 11:31:06] ...occurrences (/app/public/data/gnntrg/occurrence.tab)
[CMD] [2021-06-11 11:31:06] /usr/bin/sort /app/public/converted_csv/gnntrg_occurrences_4029.csv > /app/public/converted_csv/gnntrg_occurrences_4029.csv_sorted
[INFO] [2021-06-11 11:31:06] Converted: /app/public/converted_csv/gnntrg_occurrences_4029.csv (279289 lines)
[INFO] [2021-06-11 11:31:06] ...measurements (/app/public/data/gnntrg/measurement_or_fact.tab)
[CMD] [2021-06-11 11:31:06] /usr/bin/sort /app/public/converted_csv/gnntrg_measurements_4029.csv > /app/public/converted_csv/gnntrg_measurements_4029.csv_sorted
[INFO] [2021-06-11 11:31:08] Converted: /app/public/converted_csv/gnntrg_measurements_4029.csv (1910814 lines)
[STOP] [2021-06-11 11:31:08] convert_to_csv
[START] [2021-06-11 11:31:08] calculate_delta
[INFO] [2021-06-11 11:31:08] Looping over 3 formats...
[INFO] [2021-06-11 11:31:08] ...nodes (/app/public/data/gnntrg/taxon.tab)
[CMD] [2021-06-11 11:31:08] echo "0a" > /app/public/diff/gnntrg_nodes_4029.diff
[CMD] [2021-06-11 11:31:09] tail -n +1 /app/public/converted_csv/gnntrg_nodes_4029.csv >> /app/public/diff/gnntrg_nodes_4029.diff
[CMD] [2021-06-11 11:31:09] echo "." >> /app/public/diff/gnntrg_nodes_4029.diff
[INFO] [2021-06-11 11:31:09] Created diff: /app/public/diff/gnntrg_nodes_4029.diff (140397 lines)
[INFO] [2021-06-11 11:31:09] ...occurrences (/app/public/data/gnntrg/occurrence.tab)
[CMD] [2021-06-11 11:31:09] echo "0a" > /app/public/diff/gnntrg_occurrences_4029.diff
[CMD] [2021-06-11 11:31:09] tail -n +1 /app/public/converted_csv/gnntrg_occurrences_4029.csv >> /app/public/diff/gnntrg_occurrences_4029.diff
[CMD] [2021-06-11 11:31:09] echo "." >> /app/public/diff/gnntrg_occurrences_4029.diff
[INFO] [2021-06-11 11:31:10] Created diff: /app/public/diff/gnntrg_occurrences_4029.diff (279291 lines)
[INFO] [2021-06-11 11:31:10] ...measurements (/app/public/data/gnntrg/measurement_or_fact.tab)
[CMD] [2021-06-11 11:31:10] echo "0a" > /app/public/diff/gnntrg_measurements_4029.diff
[CMD] [2021-06-11 11:31:10] tail -n +1 /app/public/converted_csv/gnntrg_measurements_4029.csv >> /app/public/diff/gnntrg_measurements_4029.diff
[CMD] [2021-06-11 11:31:10] echo "." >> /app/public/diff/gnntrg_measurements_4029.diff
[INFO] [2021-06-11 11:31:11] Created diff: /app/public/diff/gnntrg_measurements_4029.diff (1910816 lines)
[STOP] [2021-06-11 11:31:11] calculate_delta
[START] [2021-06-11 11:31:11] parse_diff_and_store
[INFO] [2021-06-11 11:31:11] Handling diff: /app/public/diff/gnntrg_nodes_4029.diff (140397 lines)
[INFO] [2021-06-11 11:31:11] Loading nodes diff file into memory (140397 /app/public/diff/gnntrg_nodes_4029.diff lines)...
[WARN] [2021-06-11 11:31:34] Filtered Scientific Name `Heliconius egeria Cramer, 1775/76` to `Heliconius egeria Cramer, 177576`
[INFO] [2021-06-11 11:32:08] Handling diff: /app/public/diff/gnntrg_occurrences_4029.diff (279291 lines)
[INFO] [2021-06-11 11:32:08] Loading occurrences diff file into memory (279291 /app/public/diff/gnntrg_occurrences_4029.diff lines)...
[INFO] [2021-06-11 11:34:34] Handling diff: /app/public/diff/gnntrg_measurements_4029.diff (1910816 lines)
[INFO] [2021-06-11 11:34:34] Loading measurements diff file into memory (1910816 /app/public/diff/gnntrg_measurements_4029.diff lines)...
[INFO] [2021-06-11 11:52:27] Storing 173562 ScientificNames
[INFO] [2021-06-11 11:52:27] Processing group of 173562 in 174 groups of 1000
[INFO] [2021-06-11 11:53:49] Average Time: 0.468
[INFO] [2021-06-11 11:53:49] Total Time: 1m23s
[INFO] [2021-06-11 11:53:49] last 3 / first 3: 0.57
[INFO] [2021-06-11 11:53:49] Std.Dev: 0.6348228099241552; Max: 4.84
[INFO] [2021-06-11 11:53:49] Storing 173562 Nodes
[INFO] [2021-06-11 11:53:49] Processing group of 173562 in 174 groups of 1000
[INFO] [2021-06-11 11:55:26] Average Time: 0.556
[INFO] [2021-06-11 11:55:26] Total Time: 1m38s
[INFO] [2021-06-11 11:55:26] last 3 / first 3: 0.83
[INFO] [2021-06-11 11:55:26] Std.Dev: 1.5722595205626837; Max: 18.9
[INFO] [2021-06-11 11:55:26] Storing 279289 Occurrences
[INFO] [2021-06-11 11:55:26] Processing group of 279289 in 280 groups of 1000
[INFO] [2021-06-11 11:57:07] Average Time: 0.356
[INFO] [2021-06-11 11:57:07] Total Time: 1m42s
[INFO] [2021-06-11 11:57:07] last 3 / first 3: 0.78
[INFO] [2021-06-11 11:57:07] Std.Dev: 1.3553597308463905; Max: 19.71
[INFO] [2021-06-11 11:57:07] Storing 1360923 OccurrenceMetadata
[INFO] [2021-06-11 11:57:07] Processing group of 1360923 in 1361 groups of 1000
[INFO] [2021-06-11 12:00:54] Average Time: 0.162
[INFO] [2021-06-11 12:00:54] Total Time: 3m47s
[INFO] [2021-06-11 12:00:54] last 3 / first 3: 0.97
[INFO] [2021-06-11 12:00:54] Std.Dev: 0.3082207001484488; Max: 4.17
[INFO] [2021-06-11 12:00:54] Storing 1074281 Traits
[INFO] [2021-06-11 12:00:54] Processing group of 1074281 in 1075 groups of 1000
[INFO] [2021-06-11 12:10:29] Average Time: 0.528
[INFO] [2021-06-11 12:10:29] Total Time: 9m35s
[INFO] [2021-06-11 12:10:29] last 3 / first 3: 0.34
[INFO] [2021-06-11 12:10:29] Std.Dev: 0.9197825830053535; Max: 7.65
[INFO] [2021-06-11 12:10:29] Storing 153887 MetaTraits
[INFO] [2021-06-11 12:10:29] Processing group of 153887 in 154 groups of 1000
[INFO] [2021-06-11 12:10:55] Average Time: 0.17
[INFO] [2021-06-11 12:10:55] Total Time: 27s
[INFO] [2021-06-11 12:10:55] last 3 / first 3: 0.61
[INFO] [2021-06-11 12:10:55] Std.Dev: 0.09486832980505137; Max: 0.6
[STOP] [2021-06-11 12:10:55] parse_diff_and_store
[START] [2021-06-11 12:10:55] resolve_keys
[INFO] [2021-06-11 12:12:20] Occurrences to nodes (through scientific_names)...
[INFO] [2021-06-11 12:12:56] traits to occurrences...
[INFO] [2021-06-11 12:13:08] traits to nodes (through occurrences)...
[INFO] [2021-06-11 12:13:16] Traits to sex term...
[INFO] [2021-06-11 12:13:21] Traits to lifestage term...
[INFO] [2021-06-11 12:13:26] MetaTraits to traits...
[INFO] [2021-06-11 12:13:31] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-06-11 12:13:58] Assocs to occurrences...
[INFO] [2021-06-11 12:13:58] Assocs to nodes...
[INFO] [2021-06-11 12:13:58] Assoc to sex term...
[INFO] [2021-06-11 12:13:58] Assoc to lifestage term...
[INFO] [2021-06-11 12:13:58] MetaAssoc to assocs...
[STOP] [2021-06-11 12:13:58] resolve_keys
[START] [2021-06-11 12:13:58] hold_for_later_1
[STOP] [2021-06-11 12:13:58] hold_for_later_1
[START] [2021-06-11 12:13:58] hold_for_later_2
[STOP] [2021-06-11 12:13:58] hold_for_later_2
[START] [2021-06-11 12:13:58] resolve_missing_parents
[STOP] [2021-06-11 12:14:03] resolve_missing_parents
[START] [2021-06-11 12:14:03] rebuild_nodes
[START] [2021-06-11 12:14:03] Flattener#flatten
[START] [2021-06-11 12:14:03] Flattener#study_resource
[START] [2021-06-11 12:14:31] Flattener#build_ancestry
[STOP] [2021-06-11 12:16:28] Flattener#build_ancestry
[INFO] [2021-06-11 12:16:28] 173562 ancestry keys
[START] [2021-06-11 12:16:28] build_node_ancestors
[INFO] [2021-06-11 12:16:28] old ancestors deleted.
[STOP] [2021-06-11 12:18:01] build_node_ancestors
[START] [2021-06-11 12:18:06] Flattener#propagate_ancestor_ids
[STOP] [2021-06-11 12:18:30] Flattener#propagate_ancestor_ids
[STOP] [2021-06-11 12:18:30] Flattener#flatten
[STOP] [2021-06-11 12:18:30] rebuild_nodes
[START] [2021-06-11 12:18:30] resolve_missing_media_owners
[STOP] [2021-06-11 12:18:30] resolve_missing_media_owners
[START] [2021-06-11 12:18:30] sanitize_media_verbatims
[STOP] [2021-06-11 12:18:30] sanitize_media_verbatims
[START] [2021-06-11 12:18:30] queue_downloads
[STOP] [2021-06-11 12:18:30] queue_downloads
[START] [2021-06-11 12:18:30] parse_names
[WARN] [2021-06-11 12:18:30] I see 173562 names which still need to be parsed.
[WARN] [2021-06-11 12:20:45] I see 212 names which still need to be parsed.
[WARN] [2021-06-11 12:20:47] I see 5 names which still need to be parsed.
[STOP] [2021-06-11 12:20:48] parse_names
[START] [2021-06-11 12:20:48] denormalize_canonical_names_to_nodes
[STOP] [2021-06-11 12:20:51] denormalize_canonical_names_to_nodes
[START] [2021-06-11 12:20:51] match_nodes
[START] [2021-06-11 12:20:51] map_all_nodes_to_pages
[STOP] [2021-06-11 13:22:14] map_all_nodes_to_pages
[INFO] [2021-06-11 13:22:14] 21980 Unmatched nodes (of 173562)! That's too many to output. Full list in /app/public/data/gnntrg/unmatched_nodes.txt ; First 10: Canonical: Epidendrum brassavoliforme; Node#96056806; ResourceID: Epidendrum_brassavoliforme; Canonical: Cynorchis; Node#96044791; ResourceID: Cynorchis; Canonical: Aporum; Node#96010078; ResourceID: Aporum; Canonical: Habenaria ulaei; Node#96071616; ResourceID: Habenaria_ulaei; Canonical: Ophrys liebischiana; Node#96112574; ResourceID: Ophrys_liebischiana; Canonical: Ophrys pantaliciensis; Node#96112579; ResourceID: Ophrys_pantaliciensis; Canonical: Bletia; Node#96020712; ResourceID: Bletia; Canonical: Bulbophyllum schultzeanum; Node#96023730; ResourceID: Bulbophyllum_schultzeanum; Canonical: Bulbophyllum; Node#96023675; ResourceID: Bulbophyllum; Canonical: Chloraea bifasciata; Node#96033122; ResourceID: Chloraea_bifasciata
[START] [2021-06-11 13:22:14] update_nodes
[STOP] [2021-06-11 13:22:47] update_nodes
[STOP] [2021-06-11 13:22:47] match_nodes
[START] [2021-06-11 13:22:47] reindex_search
[STOP] [2021-06-11 13:25:36] reindex_search
[START] [2021-06-11 13:25:36] normalize_units
[STOP] [2021-06-11 13:26:06] normalize_units
[START] [2021-06-11 13:26:06] calculate_statistics
[STOP] [2021-06-11 13:26:12] calculate_statistics
[START] [2021-06-11 13:26:12] complete_harvest_instance
[START] [2021-06-11 13:26:12] overall_tsv_creation
[INFO] [2021-06-11 13:26:12] Processing group of 173562 in 18 batches of 10000
[INFO] [2021-06-11 13:27:32] 15395 Traits (unfiltered)...
[INFO] [2021-06-11 13:30:08] 15395 Traits (filtered)...
[INFO] [2021-06-11 13:30:11] 0 Associations (filtered)...
[INFO] [2021-06-11 13:30:23] 116983 metadata added.
[INFO] [2021-06-11 13:30:23] 0 metadata added.
[INFO] [2021-06-11 13:32:08] 15972 Traits (unfiltered)...
[INFO] [2021-06-11 13:34:47] 15972 Traits (filtered)...
[INFO] [2021-06-11 13:34:49] 0 Associations (filtered)...
[INFO] [2021-06-11 13:35:04] 125720 metadata added.
[INFO] [2021-06-11 13:35:04] 0 metadata added.
[INFO] [2021-06-11 13:36:51] 14841 Traits (unfiltered)...
[INFO] [2021-06-11 13:39:22] 14841 Traits (filtered)...
[INFO] [2021-06-11 13:39:25] 0 Associations (filtered)...
[INFO] [2021-06-11 13:39:39] 114928 metadata added.
[INFO] [2021-06-11 13:39:39] 0 metadata added.
[INFO] [2021-06-11 13:41:28] 16115 Traits (unfiltered)...
[INFO] [2021-06-11 13:44:14] 16115 Traits (filtered)...
[INFO] [2021-06-11 13:44:17] 0 Associations (filtered)...
[INFO] [2021-06-11 13:44:33] 125369 metadata added.
[INFO] [2021-06-11 13:44:33] 0 metadata added.
[INFO] [2021-06-11 13:46:22] 16120 Traits (unfiltered)...
[INFO] [2021-06-11 13:49:09] 16120 Traits (filtered)...
[INFO] [2021-06-11 13:49:12] 0 Associations (filtered)...
[INFO] [2021-06-11 13:49:25] 125260 metadata added.
[INFO] [2021-06-11 13:49:25] 0 metadata added.
[INFO] [2021-06-11 13:51:15] 15087 Traits (unfiltered)...
[INFO] [2021-06-11 13:53:54] 15087 Traits (filtered)...
[INFO] [2021-06-11 13:53:57] 0 Associations (filtered)...
[INFO] [2021-06-11 13:54:11] 117232 metadata added.
[INFO] [2021-06-11 13:54:11] 0 metadata added.
[INFO] [2021-06-11 13:56:02] 16592 Traits (unfiltered)...
[INFO] [2021-06-11 13:58:50] 16592 Traits (filtered)...
[INFO] [2021-06-11 13:58:52] 0 Associations (filtered)...
[INFO] [2021-06-11 13:59:07] 128094 metadata added.
[INFO] [2021-06-11 13:59:07] 0 metadata added.
[INFO] [2021-06-11 14:00:57] 18216 Traits (unfiltered)...
[INFO] [2021-06-11 14:04:01] 18216 Traits (filtered)...
[INFO] [2021-06-11 14:04:04] 0 Associations (filtered)...
[INFO] [2021-06-11 14:04:19] 138685 metadata added.
[INFO] [2021-06-11 14:04:19] 0 metadata added.
[INFO] [2021-06-11 14:06:13] 15457 Traits (unfiltered)...
[INFO] [2021-06-11 14:08:51] 15457 Traits (filtered)...
[INFO] [2021-06-11 14:08:53] 0 Associations (filtered)...
[INFO] [2021-06-11 14:09:09] 119227 metadata added.
[INFO] [2021-06-11 14:09:09] 0 metadata added.
[INFO] [2021-06-11 14:10:57] 15823 Traits (unfiltered)...
[INFO] [2021-06-11 14:13:38] 15823 Traits (filtered)...
[INFO] [2021-06-11 14:13:41] 0 Associations (filtered)...
[INFO] [2021-06-11 14:13:55] 124179 metadata added.
[INFO] [2021-06-11 14:13:55] 0 metadata added.
[INFO] [2021-06-11 14:15:46] 15303 Traits (unfiltered)...
[INFO] [2021-06-11 14:18:24] 15303 Traits (filtered)...
[INFO] [2021-06-11 14:18:27] 0 Associations (filtered)...
[INFO] [2021-06-11 14:18:42] 115952 metadata added.
[INFO] [2021-06-11 14:18:42] 0 metadata added.
[INFO] [2021-06-11 14:20:30] 17255 Traits (unfiltered)...
[INFO] [2021-06-11 14:23:27] 17255 Traits (filtered)...
[INFO] [2021-06-11 14:23:30] 0 Associations (filtered)...
[INFO] [2021-06-11 14:23:46] 128752 metadata added.
[INFO] [2021-06-11 14:23:46] 0 metadata added.
[INFO] [2021-06-11 14:25:36] 16048 Traits (unfiltered)...
[INFO] [2021-06-11 14:28:23] 16048 Traits (filtered)...
[INFO] [2021-06-11 14:28:26] 0 Associations (filtered)...
[INFO] [2021-06-11 14:28:40] 124285 metadata added.
[INFO] [2021-06-11 14:28:40] 0 metadata added.
[INFO] [2021-06-11 14:30:31] 16174 Traits (unfiltered)...
[INFO] [2021-06-11 14:33:20] 16174 Traits (filtered)...
[INFO] [2021-06-11 14:33:22] 0 Associations (filtered)...
[INFO] [2021-06-11 14:33:38] 125360 metadata added.
[INFO] [2021-06-11 14:33:38] 0 metadata added.
[INFO] [2021-06-11 14:35:27] 15810 Traits (unfiltered)...
[INFO] [2021-06-11 14:38:08] 15810 Traits (filtered)...
[INFO] [2021-06-11 14:38:10] 0 Associations (filtered)...
[INFO] [2021-06-11 14:38:24] 124560 metadata added.
[INFO] [2021-06-11 14:38:24] 0 metadata added.
[INFO] [2021-06-11 14:40:14] 15091 Traits (unfiltered)...
[INFO] [2021-06-11 14:42:54] 15091 Traits (filtered)...
[INFO] [2021-06-11 14:42:57] 0 Associations (filtered)...
[INFO] [2021-06-11 14:43:12] 115523 metadata added.
[INFO] [2021-06-11 14:43:12] 0 metadata added.
[INFO] [2021-06-11 14:45:01] 16825 Traits (unfiltered)...
[INFO] [2021-06-11 14:47:48] 16825 Traits (filtered)...
[INFO] [2021-06-11 14:47:51] 0 Associations (filtered)...
[INFO] [2021-06-11 14:48:08] 130696 metadata added.
[INFO] [2021-06-11 14:48:08] 0 metadata added.
[INFO] [2021-06-11 14:49:34] 7165 Traits (unfiltered)...
[INFO] [2021-06-11 14:51:08] 7165 Traits (filtered)...
[INFO] [2021-06-11 14:51:11] 0 Associations (filtered)...
[INFO] [2021-06-11 14:51:18] 54919 metadata added.
[INFO] [2021-06-11 14:51:18] 0 metadata added.
[INFO] [2021-06-11 14:51:49] Average Time: 251.448
[INFO] [2021-06-11 14:51:49] Total Time: 1h25m37s
[INFO] [2021-06-11 14:51:49] last 3 / first 3: 0.93
[INFO] [2021-06-11 14:51:49] Std.Dev: 25.014235946756397; Max: 277.39
[STOP] [2021-06-11 14:51:49] overall_tsv_creation
[INFO] [2021-06-11 14:51:49] Done. Check your files:
[INFO] [2021-06-11 14:51:49] (170966 lines) /app/public/data/gnntrg/publish_nodes.tsv
[INFO] [2021-06-11 14:51:50] (963994 lines) /app/public/data/gnntrg/publish_node_ancestors.tsv
[INFO] [2021-06-11 14:51:50] (173562 lines) /app/public/data/gnntrg/publish_scientific_names.tsv
[INFO] [2021-06-11 14:51:51] (279290 lines) /app/public/data/gnntrg/publish_traits.tsv
[INFO] [2021-06-11 14:51:51] (2155725 lines) /app/public/data/gnntrg/publish_metadata.tsv
[STOP] [2021-06-11 14:51:52] complete_harvest_instance
[START] [2021-06-11 14:51:52] completed
[STOP] [2021-06-11 14:51:52] completed
[STOP] [2021-06-11 14:51:52] logged process, took 12137.5

Latest Process

11 Jun 11:29 EXITED currently processing 0