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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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Empty overlap set! #193

Open khush876 opened 3 years ago

khush876 commented 3 years ago

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 commented 3 years ago

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

Best regards, Robert

khush876 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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