Question: remote blast requires installation of taxdb database
3
gravatar for hfan22
2.8 years ago by
hfan2240
hfan2240 wrote:

I was trying to do some remote blast. Here is my command:

blastn -query myquery.fasta -db nt -out myblast.out -remote -num_alignments 10 -outfmt "6 qacc saccver pident sscinames length mismatch gapopen evalue bitscore"

I wanted to get the scientific name instead of taxid so I requested sscinames in my output format. I am almost certain that this worked for me a few months ago (according to my work log). Today it stopped working, returning N/A for the sscinames column with warning,

Warning: [blastn] Taxonomy name lookup from taxid requires installation of taxdb database with ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz

for each query.

I would assume installing taxdb on my local computer wouldn't help.

I am using blast 2.6.0+

Any help is appreciated.

blast • 2.5k views
ADD COMMENTlink modified 14 months ago by Varshney20 • written 2.8 years ago by hfan2240

Have you emailed NCBI blast support if you are sure this has worked in the past? Perhaps there may just be some temporary glitch. They are generally responsive.

ADD REPLYlink written 2.8 years ago by genomax87k

I have the same problem. Did you find a solution?

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by tschauer0

I also have this problem Is there any update?

ADD REPLYlink written 15 months ago by marongiu.luigi520

Did you download ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz, uncompress and try putting it in the same folder as other blast indexes?

ADD REPLYlink modified 15 months ago • written 15 months ago by genomax87k

yes I did and also updated to blast 2.9 (I had 2.7). From NCBI they answered that the taxdb is required by 'sscinames' so I skipped that. I solved by grepping the taxonomy ID from the taxdb file. Less elegant but it works...

ADD REPLYlink written 15 months ago by marongiu.luigi520

Hi,

I had the same issue when I was using the remote option, I found the solution from here: getting sscinames in viral blastx query and it worked for me...

Hope this will help you.

Thanks

ADD REPLYlink written 14 months ago by Varshney20

Did you have any luck with this?

Thanks

ADD REPLYlink written 10 months ago by mrmrwinter0
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