Unknown Clair 3 model, (khz prefix)

[Brynjar-H]

Ask away!

Hello, i am trying to run the human variation pipeline on my data basecalled with: dna_r10.4.1_e8.2_5khz_400bps_sup@v4.2.0. It seems Clair3 does not recognize this model, is the only option to re-basecall the data with a version supported by Clair3? This very similar model: dna_r10.4.1_e8.2_400bps_sup@v4.2.0 is supported and by looking at the release notes i can see that at some timepoint the 5khz prefix was dropped seemingly leading to my incompatabillity. Is it generally ok to manually change the file to drop the 5khz prefix hopefully allowing Clair3 to run? Also if anyone has a suggestion on what would be the best way to do that feel free :) For reference.... ERROR ~ Error executing process > 'lookup_clair3_model (1)'

Caused by: Process lookup_clair3_model (1) terminated with an error exit status (65)

Command executed:

clair3_model=$(resolve_clair3_model.py lookup_table 'dna_r10.4.1_e8.2_5khz_400bps_sup@v4.2.0') cp -r ${CLAIR_MODELS_PATH}/${clair3_model} model echo "Basecall model: dna_r10.4.1_e8.2_5khz_400bps_sup@v4.2.0" echo "Clair3 model : ${clair3_model}"

Command exit status: 65

Command output: (empty)

Command error:

[CRITICAL ERROR] Unknown basecaller configuration.

The input basecaller configuration 'dna_r10.4.1_e8.2_5khz_400bps_sup@v4.2.0' does not have a suitable Clair3 model because the basecaller configuration has not been recognised.

Check your --basecaller_cfg has been provided correctly.

[RenzoTale88]

Hi @Brynjar-H yes, that is indeed the 5KHz model, as shown in the table here. Simply providing the model you mentioned will work.

Andrea