Question: Blast_Formatter: How To Choose Which Database To Read From?
1
gravatar for User 6228
8.8 years ago by
User 6228110
User 6228110 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 • 4.9k views
ADD COMMENTlink modified 7 weeks ago by michael0 • written 8.8 years ago by User 6228110

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 8.8 years ago by Michael Schubert6.9k

I'm getting the same error in 2.2.25+.

ADD REPLYlink written 8.5 years ago by Ryan Thompson3.4k
1
gravatar for ALchEmiXt
8.8 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 8.8 years ago by ALchEmiXt1.9k
0
gravatar for michael
7 weeks ago by
michael0
michael0 wrote:

This is years too late. However, the more recent blast releases for sure do support local databases. But the answer is not correct with respect to the notion that the reformatting from format 11 (blast archive, .asn) does not involve the original databases. This can clearly be seen if you simply open up a blast archive. It does not contain the homologous sequences of all the hits, but only the metadata. To generate the xml or html file, blast_formatter does need to query the original database.

ADD COMMENTlink written 7 weeks ago by michael0
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