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Automatic amplicon scheme selection always fails when only one scheme is available #111

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bede opened this issue Apr 25, 2024 · 1 comment · Fixed by #112
Closed

Automatic amplicon scheme selection always fails when only one scheme is available #111

bede opened this issue Apr 25, 2024 · 1 comment · Fixed by #112

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@bede
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bede commented Apr 25, 2024

When running Viridian 1.2.0 supplying a TSV containing a single custom scheme:

singularity exec viridian_workflow_v1.2.0.img viridian_workflow run_one_sample --outdir /data/test --tech ont --reads /data/reads.fastq.gz --ref_fasta /data/my-scheme.reference.fasta --amp_schemes_tsv /data/assets/my-scheme.tsv --

Assembly fails during scheme identification because the score of the best scheme cannot be compared to the absent runner up's score.

[2024-04-25T12:25:08+0100 viridian INFO] (scheme_id) Finished analysing amplicon schemes vs reads
[2024-04-25T12:25:08+0100 viridian INFO] Amplicon scheme that reads best match to: my-scheme, with score 617, and (second best)/best = None
[2024-04-25T12:25:08+0100 viridian ERROR] (second best scheme score) / (best score) is None, which is more than the required maximum 0.5
[2024-04-25T12:25:08+0100 viridian ERROR] Stopping pipeline
[2024-04-25T12:25:08+0100 viridian ERROR] Error during stage: 4/10 Detect amplicon scheme

Fortunately this can be worked around with --force_amp_scheme {scheme_name} (thanks @martinghunt )

@martinghunt
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@bede I'll be making new release 1.2.1 later this week with that fix...

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