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!