Racon/minimap2 error

I’m trying to assemble and polish my sequences from MinION.
First I used Flye to assemble, then I used Minimap2, I set the configuration of the alignment parameters to the preset option “Oxford Nanopore all-vs-all overlap mapping…” and as I don’t have a reference genome, I used the same reads (my fasta file I got from Flye) as reference genome and as dataset. Then I converted the BAM output to SAM with “BAM-to-SAM”.
After that, I used Racon and I always got the same error: “empty overlap set!”. To use Racon I use three inputs: my raw sequence in fastq, the overlaps I got from Minimap2 in SAM and the output I got from Flye in fasta.
I tried to use the ovelaps in paf. format but It didn’t work either.
Does anyone know why I always get the same error?
Thank you.

Hi @Balcala,
you wrote: I used the same reads (my fasta file I got from Flye) as reference genome and as dataset.

Racon description says: Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in SAM format.

Output of Flye is a file with contigs, not reads. It seems you need the original reads, an alignment (reads mapped to contigs) and contigs.

Kind regards,



Thank you, @igor,
I’ve tried Minimap2 with reads mapped to contigs and I’ve used that file in SAM format in Racon but It keeps saying “error: empty overlap set!”.

Hi @Balcala
I assembled a genome from nanopore reads using Flye, mapped nanopore reads to the draft assembly using minimap2, converted BAM to SAM and completed Racon on the draft assembly, nanopore reads and SAM alignment. I don’t know if it does make sense or not, because Flye has ‘built-in’ polishing step, but I cannot reproduce the error.
Kind regards,

Hi, @igor,
you were right, I mapped reads to contigs in Minimap2.
The problem that when I used Flye I applied the option “Perform metagenomic assembly”, now I’ve tried turning that option false and applying what you told me and It worked.
Thank you so much.