Ingest to phylogenetic failure during refine

[joverlee521]

Latest automated workflow failed with an error from augur refine

[batch] [2025-02-07T17:18:37+00:00] ERROR: TreeAnc.optimal_branch_length: terminal node alignments required; sequence is missing for leaf: 'A/Geoffroy_sCat/WA/24-037410-004-original/2024'. Missing terminal sequences can be inferred from sister nodes by rerunning with `reconstruct_tip_states=True` or `--reconstruct-tip-states`
[batch] [2025-02-07T17:18:37+00:00] ERROR from TreeTime: This error is most likely due to a problem with your input data.
[batch] [2025-02-07T17:18:37+00:00] Please check your input data and try again. If you continue to have problems, please open a new issue including
[batch] [2025-02-07T17:18:37+00:00] the original command and the error above:  <https://github.com/nextstrain/augur/issues/new/choose>
[batch] [2025-02-07T17:18:37+00:00] augur refine is using TreeTime version 0.11.4

[joverlee521]

Ah, similar error to #113.
The strain name is changed from A/Geoffroy'sCat/WA/24-037410-004-original/2024 to A/Geoffroy_sCat/WA/24-037410-004-original/2024 by augur tree/iqtree, so it no longer matches the sequence name in the aligned.fasta.

I totally thought I fixed this type of issue in strain names in b6f9b56 🤔

[joverlee521]

I totally thought I fixed this type of issue in strain names in b6f9b56 🤔

OH this was specifically fixed in the Andersen lab script, this new error is a NCBI GenBank record.

[jameshadfield]

The underlying Augur bug is nextstrain/augur#1084