Hello, I am following the Qiime2 tutorial “Identifying and filtering chimeric feature sequences with q2-vsearch”. I am doing this because even though I used dada2 on my data, when I went to upload my fasta file to NCBI, it flagged 1606 chimeras. When I used the commands below, I received an error message:
There was an issue with loading the file uchime-dn-out/chimeras.qza as metadata:
Metadata file path doesn’t exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): uchime-dn-out/chimeras.qza
qiime feature-table filter-features
qiime feature-table filter-seqs
qiime feature-table summarize
I have attached the chimeras.qza file. BTW, these are the exact same commands used in the tutorial with my own file names inserted.
Also, If you could also comment why I would have so many chimeras present after using the dada2 command? I did read some previous forum discussions on this but the only thing that I took away from that was that dada2 should be sufficient if you are applying it to ASV data instead of OTU data, which is what I did.