remote blast requires installation of taxdb database
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6.4 years ago
hfan22 ▴ 40

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 • 9.1k views
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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.

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

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I also have this problem Is there any update?

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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?

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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...

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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

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Did you have any luck with this?

Thanks

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