chore: update data catalog 2025-05-25

Author: dannon

catalog/build/intermediate/outbreak-taxonomy-mapping.tsv

@@ -1,25 +1,25 @@
 taxonomy_id	name	rank
+1773	Mycobacterium tuberculosis	SPECIES
 5207	Cryptococcus neoformans	SPECIES
 11050	Flaviviridae	FAMILY
-11320	Influenza A virus	
-4827	Mucorales	ORDER
-5052	Aspergillus	GENUS
-199306	Coccidioides posadasii	SPECIES
-12058	Picornaviridae	FAMILY
-5037	Histoplasma capsulatum	SPECIES
-1980415	Nairoviridae	FAMILY
-3418604	Betacoronavirus pandemicum	SPECIES
-1773	Mycobacterium tuberculosis	SPECIES
-5807	Cryptosporidium parvum	SPECIES
+11018	Togaviridae	FAMILY
+498019	Candidozyma auris	SPECIES
 1980418	Phenuiviridae	FAMILY
+5833	Plasmodium falciparum	SPECIES
 1980413	Hantaviridae	FAMILY
+11158	Paramyxoviridae	FAMILY
+199306	Coccidioides posadasii	SPECIES
+5763	Naegleria fowleri	SPECIES
+3418604	Betacoronavirus pandemicum	SPECIES
+11320	Influenza A virus	
 11266	Filoviridae	FAMILY
-11018	Togaviridae	FAMILY
 10244	Monkeypox virus	SPECIES
-5763	Naegleria fowleri	SPECIES
-1980416	Peribunyaviridae	FAMILY
-5833	Plasmodium falciparum	SPECIES
-498019	Candidozyma auris	SPECIES
-11158	Paramyxoviridae	FAMILY
+5037	Histoplasma capsulatum	SPECIES
+5807	Cryptosporidium parvum	SPECIES
+1980415	Nairoviridae	FAMILY
+12058	Picornaviridae	FAMILY
 38574	Leishmania donovani species complex	SPECIES_GROUP
+1980416	Peribunyaviridae	FAMILY
+4827	Mucorales	ORDER
 11617	Arenaviridae	FAMILY
+5052	Aspergillus	GENUS

catalog/output/qc-report.md

@@ -22,32 +22,32 @@ None
 ## Species and strain combinations with multiple taxonomy IDs
 
 - Acanthamoeba castellanii strain Neff: 1257118, 5755
-- Blumeria graminis: 1689686, 62690
-- Candida tropicalis strain MYA-3404: 5482, 294747
+- Blumeria graminis: 62690, 1689686
+- Candida tropicalis strain MYA-3404: 294747, 5482
 - Cryptococcus neoformans strain H99: 235443, 5207
 - Cryptosporidium parvum: 353152, 5807
-- Enterovirus A: 150846, 156647
+- Enterovirus A: 156647, 150846
 - Glossina fuscipes: 7396, 201502
 - Neospora caninum strain Liverpool: 29176, 572307
-- Norwalk virus: 1529918, 122929, 1529909, 122928, 1246677, 1529924, 490039
+- Norwalk virus: 1529924, 1246677, 122928, 490039, 1529918, 122929, 1529909
 - Orthoflavivirus denguei: 11069, 11053, 11070
-- Orthomarburgvirus marburgense: 448086, 3052505
+- Orthomarburgvirus marburgense: 3052505, 448086
 - Plasmodium falciparum: 5833, 36329
-- Plasmodium vinckei: 54757, 5860, 138298, 119398, 138297
+- Plasmodium vinckei: 54757, 5860, 119398, 138297, 138298
 - Trypanosoma brucei: 185431, 5702
-- Trypanosoma cruzi strain Dm28c: 5693, 85057, 1416333
-- Vesicular exanthema of swine virus: 35612, 146073
+- Trypanosoma cruzi strain Dm28c: 1416333, 5693, 85057
+- Vesicular exanthema of swine virus: 146073, 35612
 
 ## Assemblies without ploidy information
 
 None
 
 ## Outbreak descendant taxonomy IDs not found in genomes data
 
-- 3052599
-- 1980456
-- 3052686
+- 138949
+- 3052518
 - 3052560
+- 1980456
 - 463676
-- 3052518
-- 138949
+- 3052599
+- 3052686