Cannot access taxdb in local blast search

Question

[Luca Arbore]

Hi,

I succeeded in installing blast on my computer, made a database and running a blastn search. However, I would like to obtain the scientific name in the results and for this I have downloaded the taxdb. Despite copying the taxdb.btd and .bti files in the database directory along with the rest of the db files, I keep getting this: Warning: [blastn] Taxonomy name lookup from taxid requires installation of taxdb database with ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz

I have made sure that read permission of enabled, but I keep getting this message. Any ideas about why this is happening and how to proceed?

thanks a lot

[GenoMax]

made a database

Is that a custom database? If so you will need to create a map file as described here: https://www.ncbi.nlm.nih.gov/books/NBK569841/

If not, what is the exact blast+ command you are running?

[Luca Arbore]

Yes, the database is custom. I made it of .fasta obtained by searching "Phlebotominae AND COI", thus it contains only the COI mithocondrial gene of flies from this subfamily (~4845 seqs). Now, I am looking at the link sent by you and cannot figure out where I get my taxIDs, which by now I am (almost) certain they code the scientific names I need. I have also looked up the taxonomic node here https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi but obtained only the taxID of the subfamily or of the taxa above it (by checking the "full taxid lineage"). The command used was

blastn -query sandfly_coi_clean.fasta -task blastn -db db/phlebotominae -out sandfly_coi_blastn.csv -outfmt "6 qacc qlen sseqid slen  evale bitscore pident sscinames qcovs" -max_target_seqs 5 -num_threads 20

Thanks for the help