Harvest for Arctic Lichens Created 13 Nov 15:39

Harvesting Log

# Logfile created on 2019-11-13 15:39:32 -0500 by logger.rb/56815
[START] [2019-11-13 15:39:32] logged process
[START] [2019-11-13 15:39:32] create_harvest_instance
[STOP] [2019-11-13 15:39:36] create_harvest_instance
[START] [2019-11-13 15:39:36] fetch_files
[STOP] [2019-11-13 15:39:36] fetch_files
[START] [2019-11-13 15:39:36] validate_each_file
[STOP] [2019-11-13 15:39:40] validate_each_file
[START] [2019-11-13 15:39:40] convert_to_csv
[CMD] [2019-11-13 15:39:40] /usr/bin/sort /app/public/converted_csv/Arctic_Lichens_agents_18520.csv > /app/public/converted_csv/Arctic_Lichens_agents_18520.csv_sorted
[CMD] [2019-11-13 15:39:40] /usr/bin/sort /app/public/converted_csv/Arctic_Lichens_refs_18521.csv > /app/public/converted_csv/Arctic_Lichens_refs_18521.csv_sorted
[CMD] [2019-11-13 15:39:40] /usr/bin/sort /app/public/converted_csv/Arctic_Lichens_nodes_18522.csv > /app/public/converted_csv/Arctic_Lichens_nodes_18522.csv_sorted
[CMD] [2019-11-13 15:39:40] /usr/bin/sort /app/public/converted_csv/Arctic_Lichens_media_18523.csv > /app/public/converted_csv/Arctic_Lichens_media_18523.csv_sorted
[CMD] [2019-11-13 15:39:40] /usr/bin/sort /app/public/converted_csv/Arctic_Lichens_vernaculars_18524.csv > /app/public/converted_csv/Arctic_Lichens_vernaculars_18524.csv_sorted
[CMD] [2019-11-13 15:39:40] /usr/bin/sort /app/public/converted_csv/Arctic_Lichens_occurrences_18525.csv > /app/public/converted_csv/Arctic_Lichens_occurrences_18525.csv_sorted
[CMD] [2019-11-13 15:39:40] /usr/bin/sort /app/public/converted_csv/Arctic_Lichens_assocs_18526.csv > /app/public/converted_csv/Arctic_Lichens_assocs_18526.csv_sorted
[CMD] [2019-11-13 15:39:40] /usr/bin/sort /app/public/converted_csv/Arctic_Lichens_measurements_18527.csv > /app/public/converted_csv/Arctic_Lichens_measurements_18527.csv_sorted
[STOP] [2019-11-13 15:39:40] convert_to_csv
[START] [2019-11-13 15:39:40] calculate_delta
[CMD] [2019-11-13 15:39:40] echo "0a" > /app/public/diff/Arctic_Lichens_agents_18520.diff
[CMD] [2019-11-13 15:39:40] tail -n +1 /app/public/converted_csv/Arctic_Lichens_agents_18520.csv >> /app/public/diff/Arctic_Lichens_agents_18520.diff
[CMD] [2019-11-13 15:39:40] echo "." >> /app/public/diff/Arctic_Lichens_agents_18520.diff
[CMD] [2019-11-13 15:39:40] echo "0a" > /app/public/diff/Arctic_Lichens_refs_18521.diff
[CMD] [2019-11-13 15:39:40] tail -n +1 /app/public/converted_csv/Arctic_Lichens_refs_18521.csv >> /app/public/diff/Arctic_Lichens_refs_18521.diff
[CMD] [2019-11-13 15:39:40] echo "." >> /app/public/diff/Arctic_Lichens_refs_18521.diff
[CMD] [2019-11-13 15:39:40] echo "0a" > /app/public/diff/Arctic_Lichens_nodes_18522.diff
[CMD] [2019-11-13 15:39:40] tail -n +1 /app/public/converted_csv/Arctic_Lichens_nodes_18522.csv >> /app/public/diff/Arctic_Lichens_nodes_18522.diff
[CMD] [2019-11-13 15:39:40] echo "." >> /app/public/diff/Arctic_Lichens_nodes_18522.diff
[CMD] [2019-11-13 15:39:40] echo "0a" > /app/public/diff/Arctic_Lichens_media_18523.diff
[CMD] [2019-11-13 15:39:40] tail -n +1 /app/public/converted_csv/Arctic_Lichens_media_18523.csv >> /app/public/diff/Arctic_Lichens_media_18523.diff
[CMD] [2019-11-13 15:39:40] echo "." >> /app/public/diff/Arctic_Lichens_media_18523.diff
[CMD] [2019-11-13 15:39:40] echo "0a" > /app/public/diff/Arctic_Lichens_vernaculars_18524.diff
[CMD] [2019-11-13 15:39:40] tail -n +1 /app/public/converted_csv/Arctic_Lichens_vernaculars_18524.csv >> /app/public/diff/Arctic_Lichens_vernaculars_18524.diff
[CMD] [2019-11-13 15:39:40] echo "." >> /app/public/diff/Arctic_Lichens_vernaculars_18524.diff
[CMD] [2019-11-13 15:39:40] echo "0a" > /app/public/diff/Arctic_Lichens_occurrences_18525.diff
[CMD] [2019-11-13 15:39:40] tail -n +1 /app/public/converted_csv/Arctic_Lichens_occurrences_18525.csv >> /app/public/diff/Arctic_Lichens_occurrences_18525.diff
[CMD] [2019-11-13 15:39:40] echo "." >> /app/public/diff/Arctic_Lichens_occurrences_18525.diff
[CMD] [2019-11-13 15:39:40] echo "0a" > /app/public/diff/Arctic_Lichens_assocs_18526.diff
[CMD] [2019-11-13 15:39:40] tail -n +1 /app/public/converted_csv/Arctic_Lichens_assocs_18526.csv >> /app/public/diff/Arctic_Lichens_assocs_18526.diff
[CMD] [2019-11-13 15:39:40] echo "." >> /app/public/diff/Arctic_Lichens_assocs_18526.diff
[CMD] [2019-11-13 15:39:40] echo "0a" > /app/public/diff/Arctic_Lichens_measurements_18527.diff
[CMD] [2019-11-13 15:39:40] tail -n +1 /app/public/converted_csv/Arctic_Lichens_measurements_18527.csv >> /app/public/diff/Arctic_Lichens_measurements_18527.diff
[CMD] [2019-11-13 15:39:40] echo "." >> /app/public/diff/Arctic_Lichens_measurements_18527.diff
[STOP] [2019-11-13 15:39:40] calculate_delta
[START] [2019-11-13 15:39:40] parse_diff_and_store
[INFO] [2019-11-13 15:39:40] Loading agents diff file into memory (true lines)...
[INFO] [2019-11-13 15:39:40] Loading refs diff file into memory (true lines)...
[INFO] [2019-11-13 15:39:40] Loading nodes diff file into memory (true lines)...
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Calogaya arnoldii (Wedd.) Arup, Frödén & Søchting  ssp. obliterata (Pers.) Gaya` to `Calogaya arnoldii (Wedd.) Arup, Frödén & Søchting ssp. obliterata (Pers.) Gaya`
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Phaeopyxis punctum (A. Massal.) Rambold, Triebel & Coppins  ` to `Phaeopyxis punctum (A. Massal.) Rambold, Triebel & Coppins `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Arthonia nephromiaria  Nyl.` to `Arthonia nephromiaria Nyl.`
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Aspicilia  vaginans (Zahlbr.) Oxner` to `Aspicilia vaginans (Zahlbr.) Oxner`
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Bachmanniomyces uncialicola (Zopf) D. Hawksw.  ` to `Bachmanniomyces uncialicola (Zopf) D. Hawksw. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Belonia russula Körb. ex Nyl.  ` to `Belonia russula Körb. ex Nyl. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Brodoa intestiniformis (Vill.) Goward  ` to `Brodoa intestiniformis (Vill.) Goward `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Calicium viride Pers.  ` to `Calicium viride Pers. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Candelaria concolor (Dickson) Stein  ` to `Candelaria concolor (Dickson) Stein `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Catillaria subnegans  (Nyl.) Boistel` to `Catillaria subnegans (Nyl.) Boistel`
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Cecidonia umbonella (Nyl.) Triebel & Rambold  ` to `Cecidonia umbonella (Nyl.) Triebel & Rambold `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Chrysothrix chlorina (Ach.) J. R. Laundon  ` to `Chrysothrix chlorina (Ach.) J. R. Laundon `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Cystocoleus ebeneus (Dillwyn) Thwaites  ` to `Cystocoleus ebeneus (Dillwyn) Thwaites `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Dacampia hookeri (Borrer) A. Massal.  ` to `Dacampia hookeri (Borrer) A. Massal. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Dactylospora rimulicola  (Müll. Arg.) Hafellner` to `Dactylospora rimulicola (Müll. Arg.) Hafellner`
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Dermatocarpon rivulorum (Arnold) Dalla Torre & Sarnth.  ` to `Dermatocarpon rivulorum (Arnold) Dalla Torre & Sarnth. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Diploschistes scruposus (Schreb.) Norm.  ` to `Diploschistes scruposus (Schreb.) Norm. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Endocarpon pusillum Hedwig  ` to `Endocarpon pusillum Hedwig `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Epicladonia sandstedei (Zopf) D. Hawksw.  ` to `Epicladonia sandstedei (Zopf) D. Hawksw. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Epilichen scabrosus (Ach.) Clem.  ` to `Epilichen scabrosus (Ach.) Clem. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Evernia prunastri (L.) Ach.  ` to `Evernia prunastri (L.) Ach. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Gyalecta ulmi (Sw.) Zahlbr.  ` to `Gyalecta ulmi (Sw.) Zahlbr. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Gyalidea lecideopsis (A. Massal.) Lettau  ` to `Gyalidea lecideopsis (A. Massal.) Lettau `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Heppia lutosa (Ach.) Nyl.  ` to `Heppia lutosa (Ach.) Nyl. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Homostegia piggotii (Berk. & Broome) P. Karsten  ` to `Homostegia piggotii (Berk. & Broome) P. Karsten `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Icmadophila ericetorum (L.) Zahlbr.  ` to `Icmadophila ericetorum (L.) Zahlbr. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Illosporium carneum Fr.  ` to `Illosporium carneum Fr. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Immersaria athroocarpa (Ach.) Rambold & Pietschm.  ` to `Immersaria athroocarpa (Ach.) Rambold & Pietschm. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Imshaugia aleurites (Ach.) S. F. L. Meyer  ` to `Imshaugia aleurites (Ach.) S. F. L. Meyer `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Ionaspis odora (Ach.) Stein  ` to `Ionaspis odora (Ach.) Stein `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Lasallia pustulata (L.) Mérat  ` to `Lasallia pustulata (L.) Mérat `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Lecanora  vegae Malme ` to `Lecanora vegae Malme `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Lecanora  xylophila Hue` to `Lecanora xylophila Hue`
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Lecanora mughicola Nyl.  (saligna-Gruppe)` to `Lecanora mughicola Nyl. (saligna-Gruppe)`
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Lecidea commaculans Nyl.  ` to `Lecidea commaculans Nyl. `
[WARN] [2019-11-13 15:39:40] Filtered Scientific Name `Lecidoma demissum (Rutstr.) Gotth. Schneid. & Hertel  ` to `Lecidoma demissum (Rutstr.) Gotth. Schneid. & Hertel `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Leptogium teretiusculum (Wallr.) Arnold  ` to `Leptogium teretiusculum (Wallr.) Arnold `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Leptosphaerulina peltigerae (Fuckel) Riedel  ` to `Leptosphaerulina peltigerae (Fuckel) Riedel `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Lettauia cladoniicola D. Hawksw. & R. Sant.  ` to `Lettauia cladoniicola D. Hawksw. & R. Sant. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Lichenoconium xanthoriae M. S. Christ.  ` to `Lichenoconium xanthoriae M. S. Christ. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Lichenosticta alcicorniaria (Linds.) D. Hawksw.  ` to `Lichenosticta alcicorniaria (Linds.) D. Hawksw. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Lichina confinis (O. F. Müller) C. Agardh  ` to `Lichina confinis (O. F. Müller) C. Agardh `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Lithographa tesserata (DC.) Nyl.  ` to `Lithographa tesserata (DC.) Nyl. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Lopadium pezizoideum (Ach.) Körb.  ` to `Lopadium pezizoideum (Ach.) Körb. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Massalongia carnosa (Dicks.) Körb.  ` to `Massalongia carnosa (Dicks.) Körb. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Mycoblastus sanguinarius (L.) Norman  ` to `Mycoblastus sanguinarius (L.) Norman `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Mycoglaena myricae (Nyl.) R. C. Harris  ` to `Mycoglaena myricae (Nyl.) R. C. Harris `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Neolamya peltigerae  (Mont.) Theiss. & Syd.` to `Neolamya peltigerae (Mont.) Theiss. & Syd.`
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Nigropuncta rugulosa D. Hawksw.  ` to `Nigropuncta rugulosa D. Hawksw. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Normandina pulchella (Borrer) Nyl.  ` to `Normandina pulchella (Borrer) Nyl. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Ochrolechia upsaliensis (L.) A. Massal.  ` to `Ochrolechia upsaliensis (L.) A. Massal. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Parmelia sulcata Taylor  ` to `Parmelia sulcata Taylor `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Parmeliella triptophylla (Ach.) Müll. Arg.  ` to `Parmeliella triptophylla (Ach.) Müll. Arg. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Parmeliopsis hyperopta (Ach.) Arnold  ` to `Parmeliopsis hyperopta (Ach.) Arnold `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Peltigera venosa (L.) Hoffm.  ` to `Peltigera venosa (L.) Hoffm. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Pezizella epithallina (W. Phillips & Plowr.) Sacc.  ` to `Pezizella epithallina (W. Phillips & Plowr.) Sacc. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Phaeorrhiza nimbosa (Fr.) Mayrhofer & Poelt  ` to `Phaeorrhiza nimbosa (Fr.) Mayrhofer & Poelt `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Phaeosporobolus usneae D. Hawksw. & Hafellner  ` to `Phaeosporobolus usneae D. Hawksw. & Hafellner `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Phoma peltigerae (P.Karst.) D. Hawksw.  ` to `Phoma peltigerae (P.Karst.) D. Hawksw. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Phoma physciicola  Keissl.` to `Phoma physciicola Keissl.`
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Phylliscum demangeonii (Moug. & Mont.) Nyl.  ` to `Phylliscum demangeonii (Moug. & Mont.) Nyl. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Physconia perisidiosa (Erichsen) Moberg  ` to `Physconia perisidiosa (Erichsen) Moberg `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Pilophorus cereolus (Ach.) Th. Fr.  ex Hellb.` to `Pilophorus cereolus (Ach.) Th. Fr. ex Hellb.`
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Placopsis lambii Hertel & V. Wirth  ` to `Placopsis lambii Hertel & V. Wirth `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Placynthium subradiatum (Nyl.) Arnold  ` to `Placynthium subradiatum (Nyl.) Arnold `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Platismatia glauca (L.) W. L. Culb. & C. F. Culb.  ` to `Platismatia glauca (L.) W. L. Culb. & C. F. Culb. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Plectocarpon lichenum (Sommerf.) D. Hawksw.  ` to `Plectocarpon lichenum (Sommerf.) D. Hawksw. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Polychidium muscicola (Sw.) Gray  ` to `Polychidium muscicola (Sw.) Gray `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Polycoccum sporastatiae (Anzi) Arnold   ` to `Polycoccum sporastatiae (Anzi) Arnold `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Polysporina urceolata (Anzi) Brodo  ` to `Polysporina urceolata (Anzi) Brodo `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Porpidia zeoroides (Anzi) Knoph & Hertel  ` to `Porpidia zeoroides (Anzi) Knoph & Hertel `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Protoblastenia terricola (Anzi) Lynge  ` to `Protoblastenia terricola (Anzi) Lynge `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Protothelenella santessonii H. Mayrhofer  ` to `Protothelenella santessonii H. Mayrhofer `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Pseudephebe pubescens (L.) M. Choisy  ` to `Pseudephebe pubescens (L.) M. Choisy `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Psilolechia lucida (Ach.) M. Choisy  ` to `Psilolechia lucida (Ach.) M. Choisy `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Psorotichia schaereri (A. Massal.) Arnold  ` to `Psorotichia schaereri (A. Massal.) Arnold `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Pycnothelia papillaria (Ehrh.) Dufour  ` to `Pycnothelia papillaria (Ehrh.) Dufour `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Pyrenopsis subareolata Nyl.  ` to `Pyrenopsis subareolata Nyl. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Racodium rupestre Pers.  ` to `Racodium rupestre Pers. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Ramalina thrausta (Ach.) Nyl.  ` to `Ramalina thrausta (Ach.) Nyl. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Rhizoplaca chrysoleuca (Sm.) Zopf  ` to `Rhizoplaca chrysoleuca (Sm.) Zopf `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Sagiolechia protuberans (Ach.) A. Massal.  ` to `Sagiolechia protuberans (Ach.) A. Massal. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Sarcopyrenia gibba (Nyl.) Nyl.  ` to `Sarcopyrenia gibba (Nyl.) Nyl. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Sarcosagium campestre (Fr.) Poetsch & Schied.  ` to `Sarcosagium campestre (Fr.) Poetsch & Schied. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Scoliciosporum umbrinum (Ach.) Arnold  ` to `Scoliciosporum umbrinum (Ach.) Arnold `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Skyttella mulleri (Willey) D. Hawksw. & R. Sant.  ` to `Skyttella mulleri (Willey) D. Hawksw. & R. Sant. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Solorina spongiosa (Ach.) Anzi  ` to `Solorina spongiosa (Ach.) Anzi `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Sphaerophorus globosus (Huds.) Vain.  ` to `Sphaerophorus globosus (Huds.) Vain. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Sphinctrina turbinata (Pers.: Fr.) De Not.  ` to `Sphinctrina turbinata (Pers.: Fr.) De Not. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Spilonema revertens Nyl.  ` to `Spilonema revertens Nyl. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Sporastatia testudinea (Ach.) A. Massal.  ` to `Sporastatia testudinea (Ach.) A. Massal. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Squamarina lentigera (Weber) Poelt  ` to `Squamarina lentigera (Weber) Poelt `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Sticta wrightii Tuck.  ` to `Sticta wrightii Tuck. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Thamnolia vermicularis (Sw.) Schaer. var. vermicularis  ` to `Thamnolia vermicularis (Sw.) Schaer. var. vermicularis `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Umbilicaria vellea (L.) Hoffm.  ` to `Umbilicaria vellea (L.) Hoffm. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Unguiculariopsis refractiva  (Coppins) Coppins` to `Unguiculariopsis refractiva (Coppins) Coppins`
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Varicellaria rhodocarpa (Körb.) Th. Fr.  ` to `Varicellaria rhodocarpa (Körb.) Th. Fr. `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Xylographa vitiligo (Ach.) J. R. Laundon  ` to `Xylographa vitiligo (Ach.) J. R. Laundon `
[WARN] [2019-11-13 15:39:41] Filtered Scientific Name `Zwackhiomyces sphinctrinoides (Zwackh) Grube & Hafellner  ` to `Zwackhiomyces sphinctrinoides (Zwackh) Grube & Hafellner `
[INFO] [2019-11-13 15:39:41] Loading media diff file into memory (true lines)...
[INFO] [2019-11-13 15:39:41] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-11-13 15:39:41] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-11-13 15:39:41] Loading assocs diff file into memory (true lines)...
[INFO] [2019-11-13 15:39:42] Loading measurements diff file into memory (true lines)...
[INFO] [2019-11-13 15:42:07] Storing 2553 ScientificNames
[INFO] [2019-11-13 15:42:07] Processing group of 2553 in 3 groups of 1000
[INFO] [2019-11-13 15:42:08] Average Time: 0.323
[INFO] [2019-11-13 15:42:08] Total Time: 1s
[INFO] [2019-11-13 15:42:08] Storing 2553 Nodes
[INFO] [2019-11-13 15:42:08] Processing group of 2553 in 3 groups of 1000
[INFO] [2019-11-13 15:42:09] Average Time: 0.273
[INFO] [2019-11-13 15:42:09] Total Time: 1s
[INFO] [2019-11-13 15:42:09] Storing 2151 Occurrences
[INFO] [2019-11-13 15:42:09] Processing group of 2151 in 3 groups of 1000
[INFO] [2019-11-13 15:42:10] Average Time: 0.083
[INFO] [2019-11-13 15:42:10] Total Time: 1s
[INFO] [2019-11-13 15:42:10] Storing 29637 Traits
[INFO] [2019-11-13 15:42:10] Processing group of 29637 in 30 groups of 1000
[INFO] [2019-11-13 15:42:18] Average Time: 0.292
[INFO] [2019-11-13 15:42:18] Total Time: 9s
[INFO] [2019-11-13 15:42:18] last 3 / first 3: 0.8
[INFO] [2019-11-13 15:42:18] Std.Dev: 0.03162277660168379; Max: 0.43
[INFO] [2019-11-13 15:42:18] Storing 75811 MetaTraits
[INFO] [2019-11-13 15:42:18] Processing group of 75811 in 76 groups of 1000
[INFO] [2019-11-13 15:42:28] Average Time: 0.124
[INFO] [2019-11-13 15:42:28] Total Time: 10s
[INFO] [2019-11-13 15:42:28] last 3 / first 3: 0.95
[INFO] [2019-11-13 15:42:28] Std.Dev: 0.03162277660168379; Max: 0.38
[STOP] [2019-11-13 15:42:28] parse_diff_and_store
[START] [2019-11-13 15:42:28] resolve_keys
[INFO] [2019-11-13 15:42:32] Occurrences to nodes (through scientific_names)...
[INFO] [2019-11-13 15:42:33] traits to occurrences...
[INFO] [2019-11-13 15:42:33] traits to nodes (through occurrences)...
[INFO] [2019-11-13 15:42:34] Traits to sex term...
[INFO] [2019-11-13 15:42:34] Traits to lifestage term...
[INFO] [2019-11-13 15:42:34] MetaTraits to traits...
[INFO] [2019-11-13 15:42:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-11-13 15:42:36] Assocs to occurrences...
[INFO] [2019-11-13 15:42:36] Assocs to nodes...
[INFO] [2019-11-13 15:42:36] Assoc to sex term...
[INFO] [2019-11-13 15:42:36] Assoc to lifestage term...
[STOP] [2019-11-13 15:42:36] resolve_keys
[START] [2019-11-13 15:42:36] hold_for_later_1
[STOP] [2019-11-13 15:42:36] hold_for_later_1
[START] [2019-11-13 15:42:36] hold_for_later_2
[STOP] [2019-11-13 15:42:36] hold_for_later_2
[START] [2019-11-13 15:42:36] resolve_missing_parents
[STOP] [2019-11-13 15:42:36] resolve_missing_parents
[START] [2019-11-13 15:42:36] rebuild_nodes
[START] [2019-11-13 15:42:36] Flattener#flatten
[START] [2019-11-13 15:42:36] Flattener#study_resource
[START] [2019-11-13 15:42:36] Flattener#build_ancestry
[STOP] [2019-11-13 15:42:36] Flattener#build_ancestry
[INFO] [2019-11-13 15:42:36] 2553 ancestry keys
[START] [2019-11-13 15:42:36] build_node_ancestors
[INFO] [2019-11-13 15:42:36] old ancestors deleted.
[STOP] [2019-11-13 15:42:36] build_node_ancestors
[START] [2019-11-13 15:42:37] Flattener#propagate_ancestor_ids
[STOP] [2019-11-13 15:42:37] Flattener#propagate_ancestor_ids
[STOP] [2019-11-13 15:42:37] Flattener#flatten
[STOP] [2019-11-13 15:42:37] rebuild_nodes
[START] [2019-11-13 15:42:37] resolve_missing_media_owners
[STOP] [2019-11-13 15:42:37] resolve_missing_media_owners
[START] [2019-11-13 15:42:37] sanitize_media_verbatims
[STOP] [2019-11-13 15:42:37] sanitize_media_verbatims
[START] [2019-11-13 15:42:37] queue_downloads
[STOP] [2019-11-13 15:42:37] queue_downloads
[START] [2019-11-13 15:42:37] parse_names
[WARN] [2019-11-13 15:42:37] I see 2553 names which still need to be parsed.
[STOP] [2019-11-13 15:42:41] parse_names
[START] [2019-11-13 15:42:41] denormalize_canonical_names_to_nodes
[STOP] [2019-11-13 15:42:41] denormalize_canonical_names_to_nodes
[START] [2019-11-13 15:42:41] match_nodes
[START] [2019-11-13 15:42:41] map_all_nodes_to_pages
[STOP] [2019-11-13 15:45:44] map_all_nodes_to_pages
[INFO] [2019-11-13 15:45:44] 314 Unmatched nodes (of 2553)! That's too many to output. First 10: Arthonia rufidula (#54786065); Arthonia destruens (#54786295); Arthonia pannariae (#54786312); Aspicilia arctica (#54786349); Aspicilia caesiopruinosa (#54786351); Aspicilia calcarea (#54786352); Aspicilia celsii (#54786354); Aspicilia conica (#54786360); Aspicilia contigua (#54786361); Aspicilia contorta (#54786362)
[START] [2019-11-13 15:45:44] update_nodes
[STOP] [2019-11-13 15:45:45] update_nodes
[STOP] [2019-11-13 15:45:45] match_nodes
[START] [2019-11-13 15:45:45] reindex_search
[STOP] [2019-11-13 15:45:49] reindex_search
[START] [2019-11-13 15:45:49] normalize_units
[STOP] [2019-11-13 15:45:49] normalize_units
[START] [2019-11-13 15:45:49] calculate_statistics
[STOP] [2019-11-13 15:45:49] calculate_statistics
[START] [2019-11-13 15:45:49] complete_harvest_instance
[START] [2019-11-13 15:45:49] overall_tsv_creation
[INFO] [2019-11-13 15:45:49] Processing group of 2553 in 1 batches of 10000
[INFO] [2019-11-13 15:46:43] 29637 Traits (unfiltered)...
[INFO] [2019-11-13 15:46:56] 29637 Traits (filtered)...
[INFO] [2019-11-13 15:46:56] 0 Associations (filtered)...
[INFO] [2019-11-13 15:48:12] 75811 metadata added.
[INFO] [2019-11-13 15:48:12] 0 metadata added.
[INFO] [2019-11-13 15:48:12] Average Time: 120.66
[INFO] [2019-11-13 15:48:12] Total Time: 2m24s
[STOP] [2019-11-13 15:48:12] overall_tsv_creation
[INFO] [2019-11-13 15:48:12] Done. Check your files:
[INFO] [2019-11-13 15:48:12] (2553 lines) /app/public/data/Arctic_Lichens/publish_nodes.tsv
[INFO] [2019-11-13 15:48:12] (4703 lines) /app/public/data/Arctic_Lichens/publish_node_ancestors.tsv
[INFO] [2019-11-13 15:48:12] (2553 lines) /app/public/data/Arctic_Lichens/publish_scientific_names.tsv
[INFO] [2019-11-13 15:48:12] (29638 lines) /app/public/data/Arctic_Lichens/publish_traits.tsv
[INFO] [2019-11-13 15:48:12] (75812 lines) /app/public/data/Arctic_Lichens/publish_metadata.tsv
[STOP] [2019-11-13 15:48:13] complete_harvest_instance
[START] [2019-11-13 15:48:13] completed
[STOP] [2019-11-13 15:48:13] completed
[STOP] [2019-11-13 15:48:13] logged process, took 520.36

Latest Process

13 Nov 15:39 EXITED currently processing 0