Empty overlap set!

[khush876]

Hi, I am running below command to get the polished sequences from my assembly

./racon raw.fastq (pacbioreads) overlap.paf (minimap2) assembly.fast (Hifiasm file)

However, I am receiving this error message

[racon::Polisher::initialize] loaded target sequences 3.882149 s [racon::Polisher::initialize] loaded sequences 299.894416 s [racon::Polisher::initialize] error: empty overlap set!

What is the issue here?

[rvaser]

Hello, can you please paste the minimap2 command which generated the overlaps.paf file?

Best regards, Robert

[khush876]

I tried both ways:

minimap2 -c ref-genome.fasta assembly-contigs.fasta -o output.paf

minimap2 -a ref-genome.fasta assembly-contigs.fasta -o output.sam

[rvaser]

If you want to polish the assembly with reads, you need to run it like this:

minimap2 -a assembly-contigs.fasta (hifiasm file) raw.fastq (pacbioraeds) -o output.sam

Also, Racon does not parser CIGAR from paf, running minimap2 with -c will just increase the total execution time.

[khush876]

Thanks alot!!! I will try with those options suggested by you.