how to map Pacbio CCS fastq

I have a Pacbio CCS fastq like this

I want to map to genome, and this is my command and out.

I want to know how to solve it. Is this fastq correct? Thanks

It might pay to recreate the CCS reads, the qualities don’t look right – are they the same length for every read, although reads are different lengths? (this is what I would do).

Try fastqc and multiqc on the data.

If you want to continue using them and don’t care about the qualities, you can convert to FASTA using eg seqtk github.com/lh3/seqtk and map using eg blasr, minimap2 as you’ve done.