Getting taxids and scientific names in BLAST+ output

Question

[Agenor Neto]

Hi,

currently I am performing blastp in a local server, targeting RefSeq proteins database. I am getting the output in csv format with some information crucial to my workflow. One of them is taxid ("staxids" in -outfmt parameter). When I tried running BLAST with only refseq_protein, I saw that this columns was not in my results. After some research here, I discovered that I needed "taxdb" so that taxonomic informations could appear. Then, I performed some steps (following this discussion) but the results keep coming without taxids or even scinames ("sscinames") (which I don't need but also tried and it is not working). I would like to know if someone is facing the same problem and if there are other solutions to this problem. Thank you all for any help!

Answer 1

[GenoMax]

I performed some steps

Can you tell us about those? I just tested a blastp search with refseq_protein database and was able to get the taxID and names.

$ blastp -task blastp -db refseq_protein -query prot_one.fa -outfmt '6 qseqid sseqid evalue sacc staxids sscinames' 

QBM85393.1      ref|XP_025334373.1|     4.30e-107       XP_025334373    1231522 [Candida] duobushaemulonis
QBM85393.1      ref|XP_018135611.1|     2.88e-54        XP_018135611    1380566 Pochonia chlamydosporia 170
QBM85394.1      ref|XP_018709940.1|     0.0     XP_018709940    869754  Metschnikowia bicuspidata var. bicuspidata NRRL YB-4993
QBM85394.1      ref|XP_028889359.1|     1.15e-180       XP_028889359    498019  [Candida] auris