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Old 03-08-2015, 09:48 PM   #1
Location: Kansas City

Join Date: Jan 2014
Posts: 18
Default Doing local blast. No alias or index file found for nucleotide database?

I am attempting to do a local blast nt. I have implemented the following procedure:
  • nt
  • tar zvpf nt.01.tar.gz command for each volume downloaded
  • ran a simple bash command (which fails)

The command I run is as follows:
blastn -query ~/programming/blastexamples/example2/db/even_tribolium.fasta -db ~/localblastdb -task blastn -html -out out.html
blastn -query ~/programming/blastexamples/example2/db/even_tribolium.fasta -db ~/localblastdb -task blastn -html -out out.html
BLAST Database error: No alias or index file found for nucleotide database [/home/heath/localblastdb] in search path [/home/heath/programming/blastexamples/example2::]
Is the output given. At first, I thought this was because it could not read my the location of my local db. So I made sure I had appropriately extracted the tarball. I have.

Is there something wrong with my .fasta file? All I want to do is blast the local nt db against it and see what hits/matches I get. So I am quite confused as to why I am getting an error.
hyates is offline   Reply With Quote
Old 03-09-2015, 03:05 AM   #2
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Location: Denmark

Join Date: Aug 2011
Posts: 7

You haven't specified nt as the database you want to search in the command you gave. Assuming that your nt files are all in place and as they should be, and that they are located under ~/localblastdb, then try changing the -db part of the command to "-db ~/localblastdb/nt" and see if that helps.
bt27uk is offline   Reply With Quote
Old 03-09-2015, 05:22 AM   #3
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,132

You have to provide "basename" of the database you are trying to search against (in your case nt) with the -db option. As bt27uk has already pointed out above, all nt* files need to be in the same directory.
GenoMax is offline   Reply With Quote

bash, blastn, fasta, ncbi

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