I previously troubleshooted importing the nt database into qiime. I finally managed to make it work (I think?) and now I am trying to run classify-consensus-blast but I keep running into an error. I am using qiime2 version 2023.9 on the university HPC.
This is my code:
qiime feature-classifier classify-consensus-blast
--i-query CO1_rep-seqs_Truncated10.qza
--i-blastdb ~/Diet_Classifier/Import_Database_nt/full_blast_db.qza
--verbose --no-recycle --p-num-threads 12
--o-classification CO1_STG_taxonomy.qza
--o-search-results CO1_STG_BlastHits.qza
error message: There were some problems with the command: Missing option '--i-reference-taxonomy'.
I am not sure what taxonomy file it would want since I am using an imported nt database that I downloaded from NCBI. Help is greatly appreciated!
Hi @paperwolf ,
This is a very good question. The short answer: if you cannot generate a taxonomy file to accompany your blastDB, then classify-consensus-blast is probably not the correct method for you to use, as it relies on that taxonomic information to perform consensus annotation of your query sequences.
Instead, you might want to use the blast action to find the top hits for each query, not necessarily taxonomic information.
I am not sure how to extract this taxonomic information from the nt database... but altogether this is probably not the correct approach if your goal is to assign taxonomic annotations to your query sequences, as the nt database contains a very wide variety of sequences from many sources, not only e.g., marker genes used for taxonomic identification.