Hello,

I am working with FASTQ files and I want to filter them based on the alignment with references sequences in FASTA format.

I decided to use QIIME2 for this. So I imported both FASTA and FASTQ files to the required format for QIIME2 (qza artifact).

• Command to import the FASTQ files to QZA:

qiime tools import \
     --type 'SampleData[PairedEndSequencesWithQuality]' \
     --input-path manifest_file.tsv \ 
     --output-path query_sequences.qza \  
     --input-format PairedEndFastqManifestPhred33V2

• Command to import the FASTA files to QZA:

qiime tools import --input-path reference_sequences.fasta --output-path reference_sequences.qza --type 'FeatureData[Sequence]'

The problem comes when I run the command to filter the query sequences:

qiime quality-control exclude-seqs \
  --i-query-sequences query_sequences.qza \
  --i-reference-sequences reference_sequences.qza \
  --p-method blast \
  --p-perc-identity 0.90 \
  --p-perc-query-aligned 0.90 \
  --o-sequence-hits hits.qza \
  --o-sequence-misses misses.qza

This command gave the following error:

 (1/1) Invalid value for '--i-query-sequences': Expected an artifact of at
  least type FeatureData[Sequence]. An artifact of type
  SampleData[PairedEndSequencesWithQuality] was provided.

The type SampleData[PairedEndSequencesWithQuality] is the one used to import the FASTQ to QZA and the typeFeatureData[Sequence] is the one used to import the FASTA to QZA.

Is there a way to use qiime quality-control exclude-seqs directly with the FASTQ files?

Thank you very much.