Question about guppy and medaka models

[rwilton1]

Hello,

When I tried Circuitseq to basecall and assemble my plasmid data, I seemed to "lose" a lot of the data compared with when I basecalled and assembled my plasmid sequences independently. Also, the final plasmid consensus sequences had more errors than I got with my manual assembly pipeline. Although I'm using ONT barcodes, a quick glance at the sequencing_summary. txt file doesn't suggest the problem is due to barcode scoring.

I originally used the medaka model given in the downloaded run_nf_with_example_data.sh file: r1041_e82_400bps_hac_g615.
However, I reasoned that I should use the right medaka model for my data, and that might be part of my problem.

But, when I tried re-running the pipeline with a medaka model that matched my poretype (r941_min_sup_g615) it terminated with the following error (excerpt):

       Error executing process > 'MedakaConsensus (2)'

      Caused by:
        Process `MedakaConsensus (2)` terminated with an error exit status (1)
      
      Command executed:
      
        chmod -R a+rw ./
        medaka_consensus -i 03_filtered.fq.gz -d 03_chosen_assembly.fasta -o 03_racon_medaka -m r941_min_sup_g615 > file 2>&1
        chmod -R a+rw ./
       . . . . . . 

Is there another file that I need to update with the medaka model? Also, is there a way to confirm which version of guppy the pipeline is running?

Thank you!!