Hi,
Did you try the following command?
qiime tools import
–input-path sequences.fna
–output-path sequences.qza
–type ‘FeatureData[Sequence]’
If you have separate fasta file and quality file you can convert them to fastq file first using QIIME1 script
convert_fastaqual_fastq.py -f seqs.fna -q seqs.qual -o fastq_files/
If you have different naming of the files than the standard format, check out #“Fastq manifest”# formats https://docs.qiime2.org/2017.12/tutorials/importing/
kind regards,
Dorothy