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refine: warn if doing timetree and there's apparent mismatch between metadata and sequence ids #1902

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refine: warn if doing timetree and there's apparent mismatch between metadata and sequence ids #1902

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61c8f5d
refine: Warn when sequence IDs don't match metadata IDs
corneliusroemer Oct 10, 2025
9c95ef9
Update CHANGES.md for refine ID mismatch warning
corneliusroemer Oct 10, 2025
849dac6
Update augur/refine.py
corneliusroemer Oct 10, 2025
0b08c3d
Apply suggestions from code review
corneliusroemer Oct 10, 2025
8e56117
Simplify ID mismatch warning and add functional test
corneliusroemer Oct 10, 2025
3353be6
Reduce test file by generating metadata inline
corneliusroemer Oct 10, 2025
5adc31b
Fix CRAM test indentation for ID mismatch warning
corneliusroemer Oct 10, 2025
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2 changes: 2 additions & 0 deletions CHANGES.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,10 @@

## __NEXT__

* `augur refine` will now warn when building a time tree if sequence IDs in the tree don't match metadata IDs, suggesting the use of `--metadata-id-columns` to explicitly set the correct ID column. [#XXXX][] (@corneliusroemer)
* `augur curate apply-record-annotations` will now warn if an annotation was unnecessary, often indicative of the upstream data being updated. [#1893][] (@jameshadfield)

[#XXXX]: https://github.com/nextstrain/augur/pull/XXXX
[#1893]: https://github.com/nextstrain/augur/pull/1893

## 31.5.0 (17 September 2025)
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19 changes: 19 additions & 0 deletions augur/refine.py
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Expand Up @@ -309,6 +309,25 @@ def run(args):
except InvalidYearBounds as error:
raise AugurError(f"Invalid value for --year-bounds: {error}")

# Check for mismatches between sequence IDs and metadata IDs
terminal_names = {n.name for n in T.get_terminals()}
matched_ids = terminal_names & set(dates.keys())

if len(matched_ids) == 0:
print("\nWARNING: No matches found between sequence IDs in the tree and metadata IDs!", file=sys.stderr)
print(f" - Tree has {len(terminal_names)} sequences", file=sys.stderr)
print(f" - Metadata has {len(dates)} entries", file=sys.stderr)
print(f" - Metadata is using '{metadata_object.id_column}' as the ID column", file=sys.stderr)
print(f"\nThis will prevent time tree inference from working correctly.", file=sys.stderr)
print(f"You may need to explicitly set the metadata ID column using --metadata-id-columns.", file=sys.stderr)
print(f"By default, the columns {DEFAULT_ID_COLUMNS} are tried in order.\n", file=sys.stderr)
elif len(matched_ids) < len(terminal_names) * 0.5:
print(f"\nWARNING: Only {len(matched_ids)}/{len(terminal_names)} sequence IDs match metadata IDs!", file=sys.stderr)
print(f" - Metadata is using '{metadata_object.id_column}' as the ID column", file=sys.stderr)
print(f"\nThis may prevent time tree inference from working correctly.", file=sys.stderr)
print(f"You may need to explicitly set the metadata ID column using --metadata-id-columns.", file=sys.stderr)
print(f"By default, the columns {DEFAULT_ID_COLUMNS} are tried in order.\n", file=sys.stderr)

# save input state string for later export
for n in T.get_terminals():
if n.name in metadata.index and METADATA_DATE_COLUMN in metadata.columns:
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