Hi, I am trying to convert a fastq file (containing multiple sequences) to a fasta file using fastx_toolkit (Hannon lab). However I get this error message:

fastq_to_fasta: Error: invalid quality score data on line 68 (quality_tok = "ATATGCGTGCCATTG...etc)

I notice on another thread that you can put -Q33 to tell it you are using Illumina quality scores. Does anyone know if there is an equivalent flag to tell it I am using nanopore data?

If not can anyone recommend another way to convert these files?

Thank you!
You can easily do that conversion using biopython:

    from Bio import SeqIO 
    count = SeqIO.convert("input.fastq", "fastq", "output.fasta", "fasta")
    print("Converted %i records" % count)