Duplex + Polish

[strejcem]

Hi,
with Dorado 0.9.1+c8c2c9f for a bacterial genome I ran:
dorado polish --bacteria aligned_reads.sorted.bam flye/assembly.fasta > polished_assembly_corrected.fasta

which leads to
[error] Caught exception: The input BAM contains more than one read group. Please specify --RG to select which read group to process.

When I run:
dorado polish --bacteria aligned_reads.sorted.bam flye/assembly.fasta --RG test > corrected_polished.fasta
I get
[error] Caught exception: No @RG headers found in the input BAM, but user-specified RG was given. RG: 'test'

However,
samtools view -H duplex.bam

@HD     VN:1.6  SO:unknown
@PG     ID:duplex       PN:dorado       VN:0.9.1+c8c2c9f        CL:dorado duplex sup 20250120_1604_X3_FBA42844_166c12fa/pod5_skip/      DS:gpu:NVIDIA GeForce RTX 3060
@PG     ID:samtools     PN:samtools     PP:duplex       VN:1.21 CL:samtools view -H duplex.bam
@RG     ID:3d5a29885777c9915e9d68ac567fa92062b91a43_dna_r10.4.1_e8.2_400bps_sup@[email protected]        PU:FBA42844     PM:GXB03675     DT:2025-01-20T15:08:56.149+00:00        PL:ONT  DS:[email protected][email protected] runid=3d5a29885777c9915e9d68ac567fa92062b91a43     LB:VSCHT_GGE255_1a      SM:VSCHT_GGE255_1a
@RG     ID:3d5a29885777c9915e9d68ac567fa92062b91a43_dna_r10.4.1_e8.2_400bps_sup@v5.0.0  PU:FBA42844     PM:GXB03675     DT:2025-01-20T15:08:56.149+00:00        PL:ONT  DS:[email protected] runid=3d5a29885777c9915e9d68ac567fa92062b91a43       LB:VSCHT_GGE255_1a      SM:VSCHT_GGE255_1a

How should I treat polish with duplex calling?

Thanks
Michal

[strejcem]

Immediately after I wrote the issue I tried to use the ID field of the RG header which worked, at least for the simplex data.
dorado polish --bacteria aligned_reads.sorted.bam flye/assembly.fasta --RG 3d5a29885777c9915e9d68ac567fa92062b91a43_dna_r10.4.1_e8.2_400bps_sup@v5.0.0 > polished_simplex.fasta

However, duplex with --bacteria throws
[error] Caught exception: There are no bacterial models compatible with basecaller model: '[email protected][email protected]'.
and without --bacteria

[error] Selected model doesn't exist: [email protected][email protected]_polish_rl
[error] Could not download model: [email protected][email protected]_polish_rl

Also, when polishing simplex data from duplex calls it throws:
[info] Input data does not contain move tables.
dorado duplex doesn't support --emit-moves.

BTW, in the documentation it is written that we can check the mv tag using samtools. However, in mmy case with samtools 1.21
samtools view --keep-tag "mv" -c aligned_reads.sorted.bam
and
samtools view -c aligned_reads.sorted.bam
outputs the same value. But
samtools view -d "mv" -c aligned_reads.sorted.bam
outputs 0

This might be modified in the documentation.

So this is actually solved, just the documentation/error messages might be improved?

Is duplex > correct > assembly > polish --RG [simplex ID] the correct way to do it?