I've read previous posts where people had similar problems and still don't have an answer as to what is going on, so TIA!
I'm running qiime2 (q2cli version 2020.8.0) on a computing cluster. I installed it by converting the Docker container release (Docker Hub) into a Singularity container, which is compatible with computing clusters.
I'm running the following command:
qiime demux emp-paired \ --m-barcodes-file mapping.txt \ --m-barcodes-column barcode-sequence \ --p-rev-comp-mapping-barcodes \ --i-seqs $OUTPUT/emp-paired-end-sequences.qza \ --o-per-sample-sequences $OUTPUT/demux-full.qza \ --o-error-correction-details $OUTPUT/demux-details.qza \ --p-no-golay-error-correction
Sample of barcodes file:
sample-id barcode-sequence #q2:types categorical sample1 CGTACCAGATCC sample2 ATGTTTAGACGG sample3 ACATGTCACGTG sample4 CTTTAGCGCTGG sample5 CTGGTCTTACGG sample6 CAAGTCGAATAC sample7 GCAAGTGTGAGG sample8 CTCGGTCAACCA sample9 ACCCTATTGCGG sample10 TCCGTTCGTTTA sample11 ACCACCGTAACC sample12 CATTTCGCACTT sample13 TTAAGCGCCTGA
However, when I look at the output, I'm only getting 10-50 reads per sample. The barcodes are in the correct orientation, since if I remove the --p-rev-comp-mapping-barcodes flag then I get the error "No sequences were mapped to samples. Check that your barcodes are in the correct orientation."
This dataset was previously processed using a different analysis pipeline by a bioinformatics core and the median reads per sample was 45k. There are some issues with the pipeline used by the core, which is why I'm looking into processing these samples myself, but at the very least I know that there is sequence data and I am somehow losing it. I am unfamiliar with qiime2 and not sure where to start with figuring out what is going on, so thank you in advance for your help!