Thanks. These are the final commands for importing and demultiplexing, and both run with no errors.
qiime tools import --type MultiplexedPairedEndBarcodeInSequence --input-path raw-data --output-path raw-data.qza
qiime cutadapt demux-paired --i-seqs raw-data.qza --m-forward-barcodes-file metadata.tsv --m-forward-barcodes-column BarcodeSequenceForward --m-reverse-barcodes-file metadata.tsv --m-reverse-barcodes-column BarcodeSequenceReverse --o-per-sample-sequences cutadapt-demux.qza --o-untrimmed-sequences unmatched-barcodes.qza
However, I run into a new problem. Sequences are only being demultiplexed based on the F barcode. Furthermore, as the F barcodes are repeated, they are only used for demultiplexing the first time they appear in the metadata file. I’m attaching a part of metadata.tsv and the manifest obtained after demultiplexing. Could the problem be the repeated F barcodes? Why aren't the R primers being used? I tried inputing R barcodes in either 5'-3' or 3'-5' orientation. MANIFEST.txt (585 Bytes) metadata.tsv (713 Bytes)