Question: blastn cannot find the database
0
gravatar for sfcarroll
5.3 years ago by
sfcarroll70
Switzerland
sfcarroll70 wrote:

I'm new to BLAST and am trying to run a legacy blast command using blast+. I have downloaded the human_genome databases and unzipped and untarred them.

The databases are in: /home/assay/assay/bin/blast/db/human_genomic

They look like this:

human_genomic.01.nsd  human_genomic.03.nsd  human_genomic.05.nog  human_genomic.07.nni  human_genomic.09.nnd  human_genomic.11.ninhuman_genomic.01.nsi  human_genomic.03.nsi  human_genomic.05.nsd  human_genomic.07.nog  human_genomic.09.nni  human_genomic.11.nn human_genomic.00.nhd  human_genomic.01.nsq  human_genomic.03.nsq  human_genomic.05.nsi  human_genomic.07.nsd  human_genomic.09.nog  human_genomic.11.nni  .... etc ... 

There is also a human_genomic.nal file in the directory

The command line I am using & error message is:

 

$  ./legacy_blast.pl blastall -p blastn -d human_genomic -m 7 -q -2 -W 7 -e 1000 -F T

BLAST Database error: No alias or index file found for nucleotide database [human_genomic] in search path [/home/assay/assay/bin/blast/bin:/home/assay/assay/bin/blast/db:]

Program failed, try executing the command manually.

 

blast • 1.9k views
ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by sfcarroll70

I should note I am trying to blast results from Primer 3, which was run against hg19. Do I have the right database: human_genomic ?

ADD REPLYlink written 5.3 years ago by sfcarroll70
0
gravatar for sfcarroll
5.3 years ago by
sfcarroll70
Switzerland
sfcarroll70 wrote:

I resolved it.

 

The database path needs to include the name of the database directory.

Full command line:

/home/assay/assay/bin/blast/bin/legacy_blast.pl blastall -p blastn -d /home/assay/assay/bin/blast/db/human_genomic -m 7 -q -2 -W 7 -e 1000 -F T

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by sfcarroll70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2046 users visited in the last hour