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Question: remote blast requires installation of taxdb database
2
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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.

ADD COMMENTlink 2.4 years ago hfan22 • 30 • updated 8 months ago Varshney • 20
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0

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 2.4 years ago
genomax
68k
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I have the same problem. Did you find a solution?

ADD REPLYlink 2.3 years ago
tschauer
• 0
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0

I also have this problem Is there any update?

ADD REPLYlink 9 months ago
marongiu.luigi
• 380
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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?

ADD REPLYlink 9 months ago
genomax
68k
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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...

ADD REPLYlink 9 months ago
marongiu.luigi
• 380
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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

ADD REPLYlink 8 months ago
Varshney
• 20

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