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add aves, testudines and percomorpha with hardened connection retry logic - #20

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emiliorighi merged 3 commits into
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toga2
Jul 14, 2026
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add aves, testudines and percomorpha with hardened connection retry logic#20
emiliorighi merged 3 commits into
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toga2

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Registry validation

  • New rows: 1076 valid, 4 invalid
  • Manifest issues: 0
  • Duplicate assemblies (TSV files): 0
  • Duplicate URLs (TSV files): 0
  • TSV header/parse errors: 0

Inline annotations on each failing row — open Files changed for details.
Updated on every push.

Comment thread TOGA2/annotations.tsv
GCA_965278175.1 https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Aves/Alopochen_aegyptiaca__Egyptian_goose__HLaloAegy1A__GCA_965278175.1/query_annotation.gff.gz
GCA_965278775.1 https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Aves/Cygnus_cygnus__Common_whooper__HLcygCygn1A__GCA_965278775.1/query_annotation.gff.gz
GCA_965278785.1 https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Aves/Mareca_strepera__Gadwall__HLmarStre1A__GCA_965278785.1/query_annotation.gff.gz

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🚫 [annotrieve-validator] reported by reviewdog 🐶
GCA_965278785.1

  • download failed: HTTPSConnectionPool(host='genome.senckenberg.de', port=443): Max retries exceeded with url: /download/TOGA2/TOGA2integration/v1/Aves/Mareca_strepera__Gadwall__HLmarStre1A__GCA_965278785.1/query_annotation.gff.gz (Caused by NewConnectionError("HTTPSConnection(host='genome.senckenberg.de', port=443): Failed to establish a new connection: [Errno 111] Connection refused"))

Comment thread TOGA2/annotations.tsv
GCA_965278775.1 https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Aves/Cygnus_cygnus__Common_whooper__HLcygCygn1A__GCA_965278775.1/query_annotation.gff.gz
GCA_965278785.1 https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Aves/Mareca_strepera__Gadwall__HLmarStre1A__GCA_965278785.1/query_annotation.gff.gz
GCA_965278835.1 https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Aves/Alectoris_graeca__Rock_partridge__HLaleGrae1__GCA_965278835.1/query_annotation.gff.gz

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🚫 [annotrieve-validator] reported by reviewdog 🐶
GCA_965278835.1

  • download failed: HTTPSConnectionPool(host='genome.senckenberg.de', port=443): Max retries exceeded with url: /download/TOGA2/TOGA2integration/v1/Aves/Alectoris_graeca__Rock_partridge__HLaleGrae1__GCA_965278835.1/query_annotation.gff.gz (Caused by NewConnectionError("HTTPSConnection(host='genome.senckenberg.de', port=443): Failed to establish a new connection: [Errno 111] Connection refused"))

Comment thread TOGA2/annotations.tsv
GCA_965278785.1 https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Aves/Mareca_strepera__Gadwall__HLmarStre1A__GCA_965278785.1/query_annotation.gff.gz
GCA_965278835.1 https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Aves/Alectoris_graeca__Rock_partridge__HLaleGrae1__GCA_965278835.1/query_annotation.gff.gz
GCA_965285925.1 https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Aves/Acrocephalus_paludicola__aquatic_warbler__HLacrPalu1__GCA_965285925.1/query_annotation.gff.gz

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🚫 [annotrieve-validator] reported by reviewdog 🐶
GCA_965285925.1

  • download failed: HTTPSConnectionPool(host='genome.senckenberg.de', port=443): Max retries exceeded with url: /download/TOGA2/TOGA2integration/v1/Aves/Acrocephalus_paludicola__aquatic_warbler__HLacrPalu1__GCA_965285925.1/query_annotation.gff.gz (Caused by NewConnectionError("HTTPSConnection(host='genome.senckenberg.de', port=443): Failed to establish a new connection: [Errno 111] Connection refused"))

Comment thread TOGA2/annotations.tsv
GCA_045781095.1 https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Testudines/Pangshura_tecta__Indian_roofed_turtle__HLpanTect1A__GCA_045781095.1/query_annotation.gff.gz
GCA_048301635.1 https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Testudines/Deirochelys_reticularia_miaria__Western_chicken_turtle__HLdeiRetiMia1__GCA_048301635.1/query_annotation.gff.gz
GCA_050000005.1 https://genome.senckenberg.de/download/TOGA2/TOGA2integration/v1/Testudines/Podocnemis_unifilis__Yellow-spotted_Amazon_River_turtle__HLpodUnif2__GCA_050000005.1/query_annotation.gff.gz

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🚫 [annotrieve-validator] reported by reviewdog 🐶
GCA_050000005.1

  • NCBI assembly check failed: assembly accession not found in NCBI

@emiliorighi
emiliorighi merged commit 798a877 into master Jul 14, 2026
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