Harvest for Anguilla Species List Created 02 Jun 11:59

Harvesting Log

[INFO] [2021-06-02 11:59:23] Created harvest instance #3981
[STOP] [2021-06-02 11:59:23] create_harvest_instance
[START] [2021-06-02 11:59:23] fetch_files
[STOP] [2021-06-02 11:59:23] fetch_files
[START] [2021-06-02 11:59:23] validate_each_file
[INFO] [2021-06-02 11:59:23] Looping over 4 formats...
[INFO] [2021-06-02 11:59:23] ...refs (/app/public/data/anguilla_sp_list/reference.tab)
[INFO] [2021-06-02 11:59:23] Valid: /app/public/converted_csv/anguilla_sp_list_refs_3981.csv (102 lines)
[INFO] [2021-06-02 11:59:23] ...nodes (/app/public/data/anguilla_sp_list/taxon.tab)
[INFO] [2021-06-02 11:59:23] Valid: /app/public/converted_csv/anguilla_sp_list_nodes_3981.csv (1872 lines)
[INFO] [2021-06-02 11:59:23] ...occurrences (/app/public/data/anguilla_sp_list/occurrence_specific.tab)
[INFO] [2021-06-02 11:59:23] Valid: /app/public/converted_csv/anguilla_sp_list_occurrences_3981.csv (1872 lines)
[INFO] [2021-06-02 11:59:23] ...measurements (/app/public/data/anguilla_sp_list/measurement_or_fact_specific.tab)
[INFO] [2021-06-02 11:59:24] Valid: /app/public/converted_csv/anguilla_sp_list_measurements_3981.csv (6244 lines)
[STOP] [2021-06-02 11:59:24] validate_each_file
[START] [2021-06-02 11:59:24] convert_to_csv
[INFO] [2021-06-02 11:59:24] Looping over 4 formats...
[INFO] [2021-06-02 11:59:24] ...refs (/app/public/data/anguilla_sp_list/reference.tab)
[CMD] [2021-06-02 11:59:24] /usr/bin/sort /app/public/converted_csv/anguilla_sp_list_refs_3981.csv > /app/public/converted_csv/anguilla_sp_list_refs_3981.csv_sorted
[INFO] [2021-06-02 11:59:25] Converted: /app/public/converted_csv/anguilla_sp_list_refs_3981.csv (102 lines)
[INFO] [2021-06-02 11:59:25] ...nodes (/app/public/data/anguilla_sp_list/taxon.tab)
[CMD] [2021-06-02 11:59:25] /usr/bin/sort /app/public/converted_csv/anguilla_sp_list_nodes_3981.csv > /app/public/converted_csv/anguilla_sp_list_nodes_3981.csv_sorted
[INFO] [2021-06-02 11:59:26] Converted: /app/public/converted_csv/anguilla_sp_list_nodes_3981.csv (1872 lines)
[INFO] [2021-06-02 11:59:26] ...occurrences (/app/public/data/anguilla_sp_list/occurrence_specific.tab)
[CMD] [2021-06-02 11:59:26] /usr/bin/sort /app/public/converted_csv/anguilla_sp_list_occurrences_3981.csv > /app/public/converted_csv/anguilla_sp_list_occurrences_3981.csv_sorted
[INFO] [2021-06-02 11:59:27] Converted: /app/public/converted_csv/anguilla_sp_list_occurrences_3981.csv (1872 lines)
[INFO] [2021-06-02 11:59:27] ...measurements (/app/public/data/anguilla_sp_list/measurement_or_fact_specific.tab)
[CMD] [2021-06-02 11:59:27] /usr/bin/sort /app/public/converted_csv/anguilla_sp_list_measurements_3981.csv > /app/public/converted_csv/anguilla_sp_list_measurements_3981.csv_sorted
[INFO] [2021-06-02 11:59:28] Converted: /app/public/converted_csv/anguilla_sp_list_measurements_3981.csv (6244 lines)
[STOP] [2021-06-02 11:59:28] convert_to_csv
[START] [2021-06-02 11:59:28] calculate_delta
[INFO] [2021-06-02 11:59:28] Looping over 4 formats...
[INFO] [2021-06-02 11:59:28] ...refs (/app/public/data/anguilla_sp_list/reference.tab)
[CMD] [2021-06-02 11:59:28] echo "0a" > /app/public/diff/anguilla_sp_list_refs_3981.diff
[CMD] [2021-06-02 11:59:29] tail -n +1 /app/public/converted_csv/anguilla_sp_list_refs_3981.csv >> /app/public/diff/anguilla_sp_list_refs_3981.diff
[CMD] [2021-06-02 11:59:30] echo "." >> /app/public/diff/anguilla_sp_list_refs_3981.diff
[INFO] [2021-06-02 11:59:31] Created diff: /app/public/diff/anguilla_sp_list_refs_3981.diff (104 lines)
[INFO] [2021-06-02 11:59:31] ...nodes (/app/public/data/anguilla_sp_list/taxon.tab)
[CMD] [2021-06-02 11:59:31] echo "0a" > /app/public/diff/anguilla_sp_list_nodes_3981.diff
[CMD] [2021-06-02 11:59:32] tail -n +1 /app/public/converted_csv/anguilla_sp_list_nodes_3981.csv >> /app/public/diff/anguilla_sp_list_nodes_3981.diff
[CMD] [2021-06-02 11:59:33] echo "." >> /app/public/diff/anguilla_sp_list_nodes_3981.diff
[INFO] [2021-06-02 11:59:34] Created diff: /app/public/diff/anguilla_sp_list_nodes_3981.diff (1874 lines)
[INFO] [2021-06-02 11:59:34] ...occurrences (/app/public/data/anguilla_sp_list/occurrence_specific.tab)
[CMD] [2021-06-02 11:59:34] echo "0a" > /app/public/diff/anguilla_sp_list_occurrences_3981.diff
[CMD] [2021-06-02 11:59:36] tail -n +1 /app/public/converted_csv/anguilla_sp_list_occurrences_3981.csv >> /app/public/diff/anguilla_sp_list_occurrences_3981.diff
[CMD] [2021-06-02 11:59:37] echo "." >> /app/public/diff/anguilla_sp_list_occurrences_3981.diff
[INFO] [2021-06-02 11:59:38] Created diff: /app/public/diff/anguilla_sp_list_occurrences_3981.diff (1874 lines)
[INFO] [2021-06-02 11:59:38] ...measurements (/app/public/data/anguilla_sp_list/measurement_or_fact_specific.tab)
[CMD] [2021-06-02 11:59:38] echo "0a" > /app/public/diff/anguilla_sp_list_measurements_3981.diff
[CMD] [2021-06-02 11:59:39] tail -n +1 /app/public/converted_csv/anguilla_sp_list_measurements_3981.csv >> /app/public/diff/anguilla_sp_list_measurements_3981.diff
[CMD] [2021-06-02 11:59:40] echo "." >> /app/public/diff/anguilla_sp_list_measurements_3981.diff
[INFO] [2021-06-02 11:59:41] Created diff: /app/public/diff/anguilla_sp_list_measurements_3981.diff (6246 lines)
[STOP] [2021-06-02 11:59:41] calculate_delta
[START] [2021-06-02 11:59:41] parse_diff_and_store
[INFO] [2021-06-02 11:59:41] Handling diff: /app/public/diff/anguilla_sp_list_refs_3981.diff (104 lines)
[INFO] [2021-06-02 11:59:42] Loading refs diff file into memory (104 /app/public/diff/anguilla_sp_list_refs_3981.diff lines)...
[INFO] [2021-06-02 11:59:43] Handling diff: /app/public/diff/anguilla_sp_list_nodes_3981.diff (1874 lines)
[INFO] [2021-06-02 11:59:44] Loading nodes diff file into memory (1874 /app/public/diff/anguilla_sp_list_nodes_3981.diff lines)...
[INFO] [2021-06-02 11:59:46] Handling diff: /app/public/diff/anguilla_sp_list_occurrences_3981.diff (1874 lines)
[INFO] [2021-06-02 11:59:47] Loading occurrences diff file into memory (1874 /app/public/diff/anguilla_sp_list_occurrences_3981.diff lines)...
[INFO] [2021-06-02 11:59:49] Handling diff: /app/public/diff/anguilla_sp_list_measurements_3981.diff (6246 lines)
[INFO] [2021-06-02 11:59:50] Loading measurements diff file into memory (6246 /app/public/diff/anguilla_sp_list_measurements_3981.diff lines)...
[INFO] [2021-06-02 11:59:53] Storing 102 References
[INFO] [2021-06-02 11:59:53] Processing group of 102 in 1 groups of 1000
[INFO] [2021-06-02 11:59:53] Average Time: 0.05
[INFO] [2021-06-02 11:59:53] Total Time: 1s
[INFO] [2021-06-02 11:59:53] Storing 3804 ScientificNames
[INFO] [2021-06-02 11:59:53] Processing group of 3804 in 4 groups of 1000
[INFO] [2021-06-02 11:59:54] Average Time: 0.348
[INFO] [2021-06-02 11:59:54] Total Time: 2s
[INFO] [2021-06-02 11:59:54] Storing 3804 Nodes
[INFO] [2021-06-02 11:59:54] Processing group of 3804 in 4 groups of 1000
[INFO] [2021-06-02 11:59:55] Average Time: 0.258
[INFO] [2021-06-02 11:59:55] Total Time: 2s
[INFO] [2021-06-02 11:59:55] Storing 1872 Occurrences
[INFO] [2021-06-02 11:59:55] Processing group of 1872 in 2 groups of 1000
[INFO] [2021-06-02 11:59:55] Average Time: 0.115
[INFO] [2021-06-02 11:59:55] Total Time: 1s
[INFO] [2021-06-02 11:59:55] Storing 6244 Traits
[INFO] [2021-06-02 11:59:55] Processing group of 6244 in 7 groups of 1000
[INFO] [2021-06-02 11:59:57] Average Time: 0.293
[INFO] [2021-06-02 11:59:57] Total Time: 3s
[INFO] [2021-06-02 11:59:57] last 3 / first 3: 0.66
[INFO] [2021-06-02 11:59:57] Std.Dev: 0.10488088481701516; Max: 0.4
[INFO] [2021-06-02 11:59:57] Storing 2500 TraitsReferences
[INFO] [2021-06-02 11:59:57] Processing group of 2500 in 3 groups of 1000
[INFO] [2021-06-02 11:59:58] Average Time: 0.08
[INFO] [2021-06-02 11:59:58] Total Time: 1s
[INFO] [2021-06-02 11:59:58] Storing 1872 MetaTraits
[INFO] [2021-06-02 11:59:58] Processing group of 1872 in 2 groups of 1000
[INFO] [2021-06-02 11:59:58] Average Time: 0.115
[INFO] [2021-06-02 11:59:58] Total Time: 1s
[STOP] [2021-06-02 11:59:58] parse_diff_and_store
[START] [2021-06-02 11:59:58] resolve_keys
[INFO] [2021-06-02 12:00:09] Occurrences to nodes (through scientific_names)...
[INFO] [2021-06-02 12:00:14] traits to occurrences...
[INFO] [2021-06-02 12:00:14] traits to nodes (through occurrences)...
[INFO] [2021-06-02 12:00:14] Traits to sex term...
[INFO] [2021-06-02 12:00:14] Traits to lifestage term...
[INFO] [2021-06-02 12:00:14] MetaTraits to traits...
[INFO] [2021-06-02 12:00:15] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-06-02 12:00:15] Assocs to occurrences...
[INFO] [2021-06-02 12:00:15] Assocs to nodes...
[INFO] [2021-06-02 12:00:15] Assoc to sex term...
[INFO] [2021-06-02 12:00:15] Assoc to lifestage term...
[INFO] [2021-06-02 12:00:15] MetaAssoc to assocs...
[STOP] [2021-06-02 12:00:15] resolve_keys
[START] [2021-06-02 12:00:15] hold_for_later_1
[STOP] [2021-06-02 12:00:15] hold_for_later_1
[START] [2021-06-02 12:00:15] hold_for_later_2
[STOP] [2021-06-02 12:00:15] hold_for_later_2
[START] [2021-06-02 12:00:15] resolve_missing_parents
[STOP] [2021-06-02 12:00:15] resolve_missing_parents
[START] [2021-06-02 12:00:15] rebuild_nodes
[START] [2021-06-02 12:00:15] Flattener#flatten
[START] [2021-06-02 12:00:15] Flattener#study_resource
[START] [2021-06-02 12:00:15] Flattener#build_ancestry
[STOP] [2021-06-02 12:00:15] Flattener#build_ancestry
[INFO] [2021-06-02 12:00:15] 3804 ancestry keys
[START] [2021-06-02 12:00:15] build_node_ancestors
[INFO] [2021-06-02 12:00:15] old ancestors deleted.
[STOP] [2021-06-02 12:00:16] build_node_ancestors
[START] [2021-06-02 12:00:18] Flattener#propagate_ancestor_ids
[STOP] [2021-06-02 12:00:18] Flattener#propagate_ancestor_ids
[STOP] [2021-06-02 12:00:18] Flattener#flatten
[STOP] [2021-06-02 12:00:18] rebuild_nodes
[START] [2021-06-02 12:00:18] resolve_missing_media_owners
[STOP] [2021-06-02 12:00:18] resolve_missing_media_owners
[START] [2021-06-02 12:00:18] sanitize_media_verbatims
[STOP] [2021-06-02 12:00:18] sanitize_media_verbatims
[START] [2021-06-02 12:00:18] queue_downloads
[STOP] [2021-06-02 12:00:18] queue_downloads
[START] [2021-06-02 12:00:18] parse_names
[WARN] [2021-06-02 12:00:18] I see 3804 names which still need to be parsed.
[WARN] [2021-06-02 12:00:21] I see 35 names which still need to be parsed.
[STOP] [2021-06-02 12:00:22] parse_names
[START] [2021-06-02 12:00:22] denormalize_canonical_names_to_nodes
[STOP] [2021-06-02 12:00:23] denormalize_canonical_names_to_nodes
[START] [2021-06-02 12:00:23] match_nodes
[START] [2021-06-02 12:00:23] map_all_nodes_to_pages
[STOP] [2021-06-02 12:02:46] map_all_nodes_to_pages
[INFO] [2021-06-02 12:02:46] 204 Unmatched nodes (of 3804)! That's too many to output. Full list in /app/public/data/anguilla_sp_list/unmatched_nodes.txt ; First 10: Canonical: BOLD:ADI1405; Node#95602213; ResourceID: 10026424; Canonical: BOLD:ADI1406; Node#95602299; ResourceID: 10426556; Canonical: BOLD:ADQ5018; Node#95606009; ResourceID: 9995769; Canonical: Anolis; Node#95605910; ResourceID: 8782549; Canonical: Sphaerodactylus; Node#95605912; ResourceID: 8827334; Canonical: Thecadactylus; Node#95603327; ResourceID: 2445827; Canonical: Iguana; Node#95603336; ResourceID: 2459675; Canonical: Ramphotyphlops; Node#95603340; ResourceID: 2471643; Canonical: Ameiva; Node#95603342; ResourceID: 2472026; Canonical: Ameiva corax; Node#95603344; ResourceID: 2472191
[START] [2021-06-02 12:02:46] update_nodes
[STOP] [2021-06-02 12:02:48] update_nodes
[STOP] [2021-06-02 12:02:48] match_nodes
[START] [2021-06-02 12:02:48] reindex_search
[STOP] [2021-06-02 12:02:51] reindex_search
[START] [2021-06-02 12:02:51] normalize_units
[STOP] [2021-06-02 12:02:51] normalize_units
[START] [2021-06-02 12:02:51] calculate_statistics
[STOP] [2021-06-02 12:02:51] calculate_statistics
[START] [2021-06-02 12:02:51] complete_harvest_instance
[START] [2021-06-02 12:02:51] overall_tsv_creation
[INFO] [2021-06-02 12:02:51] Processing group of 3804 in 1 batches of 10000
[INFO] [2021-06-02 12:03:43] 1872 Traits (unfiltered)...
[INFO] [2021-06-02 12:04:22] 1872 Traits (filtered)...
[INFO] [2021-06-02 12:04:25] 0 Associations (filtered)...
[INFO] [2021-06-02 12:04:25] 5000 metadata added.
[INFO] [2021-06-02 12:04:25] 0 metadata added.
[INFO] [2021-06-02 12:04:52] Average Time: 90.03
[INFO] [2021-06-02 12:04:52] Total Time: 2m1s
[STOP] [2021-06-02 12:04:52] overall_tsv_creation
[INFO] [2021-06-02 12:04:52] Done. Check your files:
[INFO] [2021-06-02 12:04:53] (3804 lines) /app/public/data/anguilla_sp_list/publish_nodes.tsv
[INFO] [2021-06-02 12:04:54] (19226 lines) /app/public/data/anguilla_sp_list/publish_node_ancestors.tsv
[INFO] [2021-06-02 12:04:55] (3804 lines) /app/public/data/anguilla_sp_list/publish_scientific_names.tsv
[INFO] [2021-06-02 12:04:56] (1873 lines) /app/public/data/anguilla_sp_list/publish_traits.tsv
[INFO] [2021-06-02 12:04:57] (5001 lines) /app/public/data/anguilla_sp_list/publish_metadata.tsv
[STOP] [2021-06-02 12:04:58] complete_harvest_instance
[START] [2021-06-02 12:04:58] completed
[STOP] [2021-06-02 12:04:58] completed
[STOP] [2021-06-02 12:04:58] logged process, took 335.38

Latest Process

02 Jun 11:59 EXITED currently processing 0