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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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Error: failed to get stereo duplex models #725

Closed jadedavis5 closed 6 months ago

jadedavis5 commented 6 months ago

Hi, I am getting the following error when trying to run duplex base calling of RNA reads:

[2024-04-04 16:06:10.893] [info] > No duplex pairs file provided, pairing will be performed automatically [2024-04-04 16:06:15.209] [info] Assuming cert location is /etc/ssl/certs/ca-bundle.crt [2024-04-04 16:06:15.211] [info] - downloading rna004_130bps_sup@v3.0.1 with httplib [2024-04-04 16:06:17.231] [error] Failed to get stereo duplex model [2024-04-04 16:06:17.316] [error] No matches for chemistry: rna004_130bps, model_variant: sup, version: v3.0.1

Running with the command: dorado duplex sup --device cuda:0 --min-qscore 10 Maxmimus5_pod5_pass/ > Maximus5.duplex.bam

I have tried pre-processing files with the pod5 suggestions and still the same error. I have also tried running specifically putting rna004_130bps_sup@v3.0.1 instead of sup.

HalfPhoton commented 6 months ago

Hi @jadedavis5, Duplex basecalling RNA is not possible with (single-stranded) RNA and the error you're seeing is because dorado cannot find duplex models for RNA.

Kind regards, Rich

jadedavis5 commented 6 months ago

Thanks for the quick response!