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Automated h5n1-cattle-outbreak phylo build failure #113

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joverlee521 opened this issue Dec 30, 2024 · 2 comments · Fixed by #114
Closed

Automated h5n1-cattle-outbreak phylo build failure #113

joverlee521 opened this issue Dec 30, 2024 · 2 comments · Fixed by #114
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@joverlee521
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Error from augur refine

[batch] [2024-12-30T18:13:29+00:00] ERROR: TreeAnc.optimal_branch_length: terminal node alignments required; sequence is missing for leaf: 'A/PETFOOD/USA_OR/24-037325-011/2024'. Missing terminal sequences can be inferred from sister nodes by rerunning with `reconstruct_tip_states=True` or `--reconstruct-tip-states`
[batch] [2024-12-30T18:13:29+00:00] ERROR from TreeTime: This error is most likely due to a problem with your input data.
@joverlee521 joverlee521 self-assigned this Dec 30, 2024
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I could not find the strain name A/PETFOOD/USA_OR/24-037325-011/2024 in results/h5n1-cattle-outbreak/ha/default/aligned.fasta, but when I searched for PETFOOD, I found the strain A/PETFOOD/USA:OR/24-037325-011/2024.

So there's a mismatch of strain name:

strain name file
A/PETFOOD/USA:OR/24-037325-011/2024 results/h5n1-cattle-outbreak/ha/default/aligned.fasta
A/PETFOOD/USA_OR/24-037325-011/2024 results/h5n1-cattle-outbreak/ha/default/tree-raw.nwk

The mismatch is caused by the strain name being modified by iqtree during augur tree (nextstrain/augur#1084).

@joverlee521
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A/PETFOOD/USA:OR/24-037325-011/2024 is a constructed strain name for an SRA record ingested by the Andersen lab, so I'll do a couple things to update the data:

  1. Update construct_strain_name to align with iqtree's renameString to avoid the invalid characters
  2. Update create_new_record to parse the country field to account for locations such as USA:OR.

joverlee521 added a commit that referenced this issue Dec 30, 2024
@joverlee521
curate-andersen-lab-data: Replace invalid characters in strain name
b6f9b56 
Replace invalid characters with `_` to match iqtree¹ so augur tree will
not modify strain names and cause a mismatch between the tree and the
alignment FASTA.²

Keeps the previous removal of whitespace in place to ensure that the
previous valid strain names do not change.

¹ <https://github.com/iqtree/iqtree2/blob/74da454bbd98d6ecb8cb955975a50de59785fbde/utils/tools.cpp#L607>
² <#113>
joverlee521 added a commit that referenced this issue Dec 30, 2024
@joverlee521
curate-andersen-lab-data: Parse county as GenBank location
234c110 
Use the augur.curate.parse_genbank_location function to parse the
country field since we've now seen an example of it formatted as
the GenBank geolocation format ("USA:OR") in the SRA data.¹

¹ <#113>
@joverlee521 joverlee521 mentioned this issue Dec 30, 2024
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@joverlee521 joverlee521 mentioned this issue Feb 7, 2025
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Improve ingest for Andersen lab/SRA sequences nextstrain/avian-flu
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