Question: Problems setting up nt blast database
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gravatar for goatsrunfaster
6 weeks ago by
goatsrunfaster20 wrote:

I am pulling my hair out trying to simply set up blast on my university server system. I downloaded all 36 of the packaged nt database files from the ncbi ftp site (nt.00-nt.35), and put them in the following folder: /network/rit/lab/andamlab/bin/ncbi-blast-2.10.1+/blast/db

I then added this path to my bash profile, but when I run the following:

blastn -db db -query GCF_006334995.1_ASM633499v1_genomic.fna -out blast_results.out

I get this:

BLAST Database error: No alias or index file found for nucleotide database [db] in search path [/network/rit/lab/andamlab/jrmatthews/UNH_Data_Streptomyces/streptomyces:/network/rit/lab/andamlab/bin/ncbi-blast-2.10.1+/blast/db:]

The db folder contains no subdirectories and everything is unpacked, I have also confirmed there is a .nal file there as well? What am I missing here?

Any help is greatly appreciated!

software error • 113 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by goatsrunfaster20
0
gravatar for goatsrunfaster
6 weeks ago by
goatsrunfaster20 wrote:

I figured it out, I didnt realize the -db option had to be the .nal file name (which in this case was env_nt)

ADD COMMENTlink written 6 weeks ago by goatsrunfaster20
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