Not sure if anyone can help me with a Racon issue as the developers are not very responsive on GitHub. I am trying to assemble a genome without a reference. I first did basecalling using dorado, then converted from bam to fastq using samtools, then trimmed using nanofilt from there I used flye for assembly and then ran minimap2 to get my sam file. For some reason when I then run Racon, I get the following error:

[racon::Polisher::initialize] loaded target sequences 0.000226 s
[racon::Polisher::initialize] loaded sequences 0.034854 s
[racon::Polisher::initialize] error: empty overlap set!

I used the following command to run the assembly:

flye --nano-raw sample_id.trimmed.fastq -o assembly -I 3 -t 4

I used the following command to run minimap2:

minimap2 -ax map-ont -t 4 sample_id.trimmed1.fastq assembly/assembly.fasta > sample_id.sam

I then used the following command to run racon:

racon -m 8 -x -8 -g -6 -w 500 -t 4 sample_id.trimmed1.fastq sample_id.sam assembly/assembly.fasta > Racon_polished.fasta

Could I please get some assistance on this issue as I am not sure what I am doing wrong. Thank you

First lines of the assembled fasta file:


First lines of the trimmed fastq file:


First lines of the sam file:

contig_1    0   08ef4187-c2ab-4756-a269-275f6dfe99af    1   60  93179S96M1I81M1D29M1I10M2I420M1I118M1I107M1D63M1I18M4I660M2I242M CTAACTGTATTGCTGGGAAACAAATCAA


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