augur export v2 --tree results/tree.nwk --metadata data/L4_nextstrain.tsv --node-data results/branch_lengths.json results/traits.json results/drms.json results/aa_muts.json results/nt_muts.json results/clades.json --auspice-config config/auspice_config.json --colors config/color.tsv --lat-longs config/lat_longs.tsv --output auspice/tb.json
Validating schema of ‘results/aa_muts.json’…
Validating schema of ‘results/nt_muts.json’…
Validating config file config/auspice_config.json against the JSON schema
Validating schema of ‘config/auspice_config.json’…
WARNING: [config file] Trait ‘Capreomycin’ is missing type information. We’ve guessed ‘categorical’.
WARNING: [config file] Trait ‘Pyrazinamide’ is missing type information. We’ve guessed ‘categorical’.
WARNING: [config file] Trait ‘Drug_Resistance’ is missing type information. We’ve guessed ‘continuous’.
WARNING: [config file] Trait ‘Isoniazid’ is missing type information. We’ve guessed ‘categorical’.
WARNING: [config file] Trait ‘Fluoroquinolones’ is missing type information. We’ve guessed ‘categorical’.
WARNING: [config file] Trait ‘Ethionamide’ is missing type information. We’ve guessed ‘categorical’.
WARNING: [config file] Trait ‘Streptomycin’ is missing type information. We’ve guessed ‘categorical’.
WARNING: [config file] Trait ‘Ethambutol’ is missing type information. We’ve guessed ‘categorical’.
WARNING: [config file] Trait ‘Rifampicin’ is missing type information. We’ve guessed ‘categorical’.
WARNING: [config file] Trait ‘Amikacin’ is missing type information. We’ve guessed ‘categorical’.
WARNING: country->Netherland did not have an associated lat/long value (matching performed in lower case). Auspice won’t be able to display this location.
WARNING: region->Asia did not have an associated lat/long value (matching performed in lower case). Auspice won’t be able to display this location.
Validating produced JSON
Validating schema of ‘auspice/tb.json’…
.tree {“name”: “NODE_0000015”, “node_attrs”: {“div”: 0…} failed oneOf validation for [{“$ref”: “#/$defs/tree”}, {“type”: “array”, “minItems”: 1, “items”: {“$ref”: “#/$defs/tree”}}]
validation for arm 0: {“$ref”: “#/$defs/tree”}
.tree.children[…].branch_attrs.mutations {“nuc”: [“G50100C”, “G126080C”, “C192250T”, "C24…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C54952T”, “T68085A”, “C118648T”, "C136…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“G414A”, “C63843G”, “G139081A”, "G16912…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C49586T”, “A59781G”, “A92639G”, "C1592…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C50585T”, “G118701T”, “G234021A”, “G63…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“G38416T”, “G60010C”, “G62340T”, “G6635…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“G2961C”, “G4326C”, “C27499G”, “C43105T…} failed additionalProperties validation for false
.tree.branch_attrs.mutations {”*MtCM”: [“A58X”, “K60X”, “S111X”, “N141X”, “R1…} failed additionalProperties validation for false
validation for arm 1: {“type”: “array”, “minItems”: 1, “items”: {”$ref”: “#/$defs/tree”}}
.tree {“name”: “NODE_0000015”, “node_attrs”: {“div”: 0…} failed type validation for “array”
Validation of ‘auspice/tb.json’ failed.
Validation of auspice/tb.json failed. Please check this in a local instance of auspice, as it is not expected to display correctly.