.meta.genome_annotations failed additionalProperties validation for false

Help and Getting Started
1

Hello!
Upon running augur export v2, I get the error below.
The previous steps of the pipeline, which are ‘augur tree’, ‘augur refine’, ‘augur traits’, ‘augur ancestral’, ‘augur translate’, ‘augur clades’, don’t show me any error. Can anyone, please, help me with that?
Thank you!

.meta.genome_annotations {“nuc”: {“end”: 197205, “start”: 1, “strand”: “+…} failed additionalProperties validation for false
.tree {“name”: “NODE_0000000”, “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”: [“-1157T”, “-1158G”, “-1159T”, “-1160A”,…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“T1157-”, “G1158-”, “T1159-”, “A1160-”,…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C11916T”, “G15856A”, “C47782T”, "C8842…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“T28389G”, “A28395C”, “C28404G”, “T4049…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“G35669A”, “G131576-”, “C131577-”, “T13…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“G47783A”, “T131595-”], “A25R”: [”665X…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“G2215A”, “G32368A”, “C127102T”, “T1315…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [”-5492T”, “C47782T”, “-131597T”, "-1717…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C57137T”, “G121936T”], “A15.5L”: ["Y2…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C121914T”, “-131596T”, “-131597T”, "-1…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“T37832A”, “C40527T”], “C18L”: [“D407V”…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C32349T”, “C40553T”, “-177574A”, "-177…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C34529-”, “G36061-”, “C38369-”, "C3968…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“A208-”, “T2810-”, “T4712-”, “T4792-”, …} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C47782T”], “F4.5R”: [“R74*”]} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“G6476A”, “C18507T”, “C47782T”], "F4.5R…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“G850A”, “A6565-”, “A15113-”, “A19592-”…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C47782T”], “F4.5R”: [“R74*”]} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C21499T”, “C47782T”, “C123012T”], "F4.…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C47594T”, “C101751T”, “G120514A”, "G12…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C139776T”], “A32.5L”: [“E2K”]} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C121914T”, “C158919T”], “A15.5L”: ["A1…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“T37911-”, “A37912-”, “T37913-”, "A4789…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“T5492-”, “G169688A”, “A171721-”, "A171…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“G25168A”, “G56624A”, “G139670A”, "T152…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“C47605T”, “G118485A”, “-171767A”, “-17…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“A29570G”, “G169913A”], “B1O.5R”: [“R84…} failed additionalProperties validation for false
.tree.children[…].branch_attrs.mutations {“nuc”: [“A208-”, “T2810-”, “T4195-”, “G4632-”, …} failed additionalProperties validation for false
validation for arm 1: {“type”: “array”, “minItems”: 1, “items”: {”$ref”: “#/$defs/tree”}}
.tree {“name”: “NODE_0000000”, “node_attrs”: {“div”: 0…} failed type validation for “array”
Validating schema of ‘data/nt_muts.json’…
Validating schema of ‘data/aa_muts.json’…
Validating config file config/auspice_config.json against the JSON schema
Validating schema of ‘config/auspice_config.json’…
WARNING: geo-coordinate file contains invalid line. Please make sure not to mix tabs and spaces as delimiters (use only tabs): covv_b_Country U.S. Minor Outlying Islands

Validating produced JSON
Validating schema of ‘MPxV_Global.json’…
Validation of ‘MPxV_Global.json’ failed.

Validation of MPxV_Global.json failed. Please check this in a local instance of auspice, as it is not expected to display correctly.

1 Like
2

Hi @opalmeira! I’d be happy to help. I haven’t seen this error before. Would it be possible for you to post the following so I can try to reproduce your issue and help fix it?

  1. The exact augur export command that snakemake (I assume you use snakemake) runs (you can get that command by adding -p to the invocation nextstrain or snakemake depending on what you use
    By exact command I mean something like this:
augur export v2       --tree results/europe/tree.nwk             --metadata results/europe/metadata_adjusted.tsv.xz             --node-data results/europe/branch_lengths.json results/europe/nt_muts.json results/europe/aa_muts.json   --include-root-sequence             --colors results/europe/colors.tsv             --lat-longs defaults/lat_longs.tsv                  --output results/europe/ncov_with_accessions.json --skip-validation
  1. All input files to the exact command you ran, that means every file that is part of the export command, in the above example:
  • results/europe/tree.nwk
  • results/europe/metadata_adjusted.tsv.xz
  • results/europe/branch_lengths.json
  • etc.
  1. The version of augur you’re using, that is the output of augur version
  2. A short explanation of how you run the workflow (via nextstrain or snakemake, whether you use docker, conda, etc.)

If some of the input data cannot be shared here via the forum, e.g. because it is GISAID data, you can send the files in question also to cornelius.roemer@unibas.ch as attachment.

Best, Cornelius

3

This appears to me to be due to the characters used in the genome annotation names here, e.g. gene/region names like A15.5L. Our data schema for those does not allow periods (.). We’ve considered expanding this to be less restrictive while still accounting for limitations in other parts of the software ecosystem.

2 Likes
4

I have the same problem with augur 24.2.1


 Nextstrain  ~/build $ augur export v2             --tree results/tree.nwk             --metadata results/filtered_metadata.tsv             --auspice-config resources/auspice_config.json             --node-data results/muts.json results/branch_lengths.json results/dummy_clades.json             --output results/auspice.json
Validating schema of 'results/muts.json'...
Validating config file resources/auspice_config.json against the JSON schema
Validating schema of 'resources/auspice_config.json'...
WARNING: Requested color-by field 'Isolate Lineage' does not exist and will not be used as a coloring or exported.

WARNING: Requested color-by field 'Geographic Region' does not exist and will not be used as a coloring or exported.

WARNING: Requested color-by field 'Geographic Location' does not exist and will not be used as a coloring or exported.

WARNING: Requested color-by field 'Release Date' does not exist and will not be used as a coloring or exported.

WARNING: Requested color-by field 'Submitter Affiliation' does not exist and will not be used as a coloring or exported.

WARNING: Requested color-by field 'Submitter Names' does not exist and will not be used as a coloring or exported.

Validating produced JSON
Validating schema of 'results/auspice.json'...
  .tree {"name": "NODE_0000000", "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": ["C365T", "G767A", "A953G", "A1136G", "T…} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["A87G", "G641A", "A839G", "A860G", "C10…} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["T506C", "C548T", "G641A", "C963T", "C1…} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["G326A", "G767A", "A785G", "T1181C", "C…} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["C986A", "C1079T", "G1322T", "C1532A", …} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["G530A", "C963T", "G1025A", "A1429G", "…} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["A572G", "C1034T", "G1076A", "G1304A", …} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["A28G", "A45T", "A554G", "T1223C", "G12…} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["C106T", "A149G", "A260G", "A269G", "C2…} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["T333C", "C353T", "A452G", "A563G", "G1…} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["T104C", "T324C", "G326A", "T380C", "C5…} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["T24C", "C659T", "T833C", "T881C", "G14…} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["C215T", "T263C", "T332C", "C653T", "G7…} failed additionalProperties validation for false
      .tree.children[…].branch_attrs.mutations {"nuc": ["T100C", "C218T", "T236C", "G362A", "C3…} failed additionalProperties validation for false
      .tree.children[1].branch_attrs.mutations {"nuc": ["C42A", "C170T", "T185C", "C285T", "G31…} failed additionalProperties validation for false
      .tree.branch_attrs.mutations {"nuc": ["G17A", "A42C", "T215C", "T218C", "T269…} failed additionalProperties validation for false
    validation for arm 1: {"type": "array", "minItems": 1, "items": {"$ref": "#/$defs/tree"}}
      .tree {"name": "NODE_0000000", "node_attrs": {"div": 0…} failed type validation for "array"
Validation of 'results/auspice.json' failed.

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Validation of results/auspice.json failed. Please check this in a local instance of `auspice`, as it is not expected to display correctly.