error: empty overlap set!

[mmnascimento]

Hi!

For a bit of background, I am trying to assemble a viral genome with nanopore data and illumina data. I assembled the Nanopore data with flye, then used racon twice (successfully), and then medaka twice -> all with just the nanopore data.

After these steps I planned on using racon with the illumina data. I used the script pointed out in another empty overlap issue thread here to join and rename my illumina reads. Then i used minimap as follows:

minimap2 -ax sr ./analysis/medaka/2/output/consensus.fasta ./analysis/Illumina_data/eehv5_illumina_data.fastq > ./analysis/Illumina_data/medaka2_illumina_data.sam

And then racon:

racon ./analysis/medaka/2/output/consensus.fasta ./analysis/Illumina_data/medaka2_illumina_data.sam ./analysis/Illumina_data/eehv5_illumina_data.fastq

But I keep getting the same error:

[racon::Polisher::initialize] loaded target sequences 166.953096 s
[racon::Polisher::initialize] loaded sequences 0.729270 s
[racon::Polisher::initialize] error: empty overlap set!

Any suggestions on how to solve this?