Question: Blast_Formatter: How To Choose Which Database To Read From?
1
gravatar for User 6228
7.8 years ago by
User 6228100
User 6228100 wrote:

Hi, I am attempting to use the blast_formatter included with Blast+ 2.2.24 to convert a blast archive file to xml format. However, I get this error message when I run the command:

BLAST Database error: Nucleotide BLAST database 'beij' does not exist in the NCBI servers

Here is the command I'm running:

blast_formatter -archive beij_archive.asn -outfmt 5 -out beij_archive.xml

I tried this:

blast_formatter -db $HOME"/beijerinckia_indica_subsp_indica_atcc_9039/beij" \
-archive beij_archive.asn -outfmt 5 -out beij.xml

But I get an error that db is not a supported option. How do I specify the local DB I used to generate the archive file? Or is there something I'm missing.

Thanks for your help!

blast • 4.4k views
ADD COMMENTlink written 7.8 years ago by User 6228100

As blast_formatter is relatively new and it does not seem to support local databases in 2.2.23+, maybe there is still a bug in 2.2.24+. Have you tried it with the newest one as well?

ADD REPLYlink written 7.8 years ago by Michael Schubert6.9k

I'm getting the same error in 2.2.25+.

ADD REPLYlink written 7.5 years ago by Ryan Thompson3.4k
1
gravatar for ALchEmiXt
7.7 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

You might want to check this documentation: http://www.ncbi.nlm.nih.gov/books/NBK1763/ The blast_formatter utility formats BLAST RESULT ARCHIVES being output by the -outfmt 11 parameter. Its usages is more or less explained at paragraph 5.8 and doesn't seem to involve the original BLAST database anymore. At least that is what I make up from the docs.

ADD COMMENTlink written 7.7 years ago by ALchEmiXt1.9k
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