Augur 26 breaks 21L workflow due to duplicate sequences erroring in augur filter

[corneliusroemer]

Related to nextstrain/augur#1613

Error happens here:
https://github.com/nextstrain/ncov/actions/runs/11164069511/job/31032539057#step:5:12039

[batch] [2024-10-03T16:24:15+00:00] ERROR: The following strains are duplicated in 'results/gisaid_21L_aligned.fasta.zst':
[batch] [2024-10-03T16:24:15+00:00] Wuhan/Hu-1/2019
[batch] [2024-10-03T16:24:15+00:00] ================================================================================
[batch] [2024-10-03T16:24:39+00:00] ERROR: The following strains are duplicated in 'results/gisaid_21L_aligned.fasta.zst':
[batch] [2024-10-03T16:24:39+00:00] Wuhan/Hu-1/2019
[batch] [2024-10-03T16:24:40+00:00] [Thu Oct  3 16:24:39 2024]
[batch] [2024-10-03T16:24:40+00:00] Error in rule combine_samples:
[batch] [2024-10-03T16:24:40+00:00]     jobid: 863
[batch] [2024-10-03T16:24:40+00:00]     input: results/gisaid_21L_aligned.fasta.zst, results/gisaid_21L_metadata.tsv.zst, results/oceania_6m/sample-focal_early.txt, results/oceania_6m/sample-context_early.txt, results/oceania_6m/sample-focal_recent.txt, results/oceania_6m/sample-context_recent.txt
[batch] [2024-10-03T16:24:40+00:00]     output: results/oceania_6m/oceania_6m_subsampled_sequences.fasta.xz, results/oceania_6m/oceania_6m_subsampled_metadata.tsv.xz
[batch] [2024-10-03T16:24:40+00:00]     log: logs/subsample_regions_oceania_6m.txt (check log file(s) for error details)
[batch] [2024-10-03T16:24:40+00:00]     conda-env: /nextstrain/build/.snakemake/conda/ef7f392b0ecf86741cd7c0bee42f4f0e_
[batch] [2024-10-03T16:24:40+00:00]     shell:
[batch] [2024-10-03T16:24:40+00:00]         
[batch] [2024-10-03T16:24:40+00:00]         augur filter \
[batch] [2024-10-03T16:24:40+00:00]             --sequences results/gisaid_21L_aligned.fasta.zst \
[batch] [2024-10-03T16:24:40+00:00]             --metadata results/gisaid_21L_metadata.tsv.zst \
[batch] [2024-10-03T16:24:40+00:00]             --exclude-all \
[batch] [2024-10-03T16:24:40+00:00]             --include results/oceania_6m/sample-focal_early.txt results/oceania_6m/sample-context_early.txt results/oceania_6m/sample-focal_recent.txt results/oceania_6m/sample-context_recent.txt \
[batch] [2024-10-03T16:24:40+00:00]             --output-sequences results/oceania_6m/oceania_6m_subsampled_sequences.fasta.xz \
[batch] [2024-10-03T16:24:40+00:00]             --output-metadata results/oceania_6m/oceania_6m_subsampled_metadata.tsv.xz 2>&1 | tee logs/subsample_regions_oceania_6m.txt
[batch] [2024-10-03T16:24:40+00:00]         
[batch] [2024-10-03T16:24:40+00:00]         (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
[batch] [2024-10-03T16:24:40+00:00] Logfile logs/subsample_regions_oceania_6m.txt:
[batch] [2024-10-03T16:24:40+00:00] ================================================================================
[batch] [2024-10-03T16:24:40+00:00] ERROR: The following strains are duplicated in 'results/gisaid_21L_aligned.fasta.zst':
[batch] [2024-10-03T16:24:40+00:00] Wuhan/Hu-1/2019

@victorlin could you possibly have a look at fixing this since you introduced the breaking change in Augur so you might know best how to work around it.

[joverlee521]

Looks like @victorlin fixed the issue in #1154 and the automated run for the 21L build completed successfully yesterday.

[tsibley]

Noting this is a duplicate of #1153.