Question: Blastn And Blastcmd Issues - Blast
0
gravatar for Andrewktmeikle
7.7 years ago by
Glasgow
Andrewktmeikle0 wrote:

Hey all, first of all I'd just to say that I am fairly new to the field of bioinformatics and I'm, unfortunately, learning by my mistakes more than my successes atm and I'm having some trouble executing a query on a database I created through using blastdbcmd

Then command i'm trying to run is

<Code>
blastn -wordsize 11 -reward 2 -penalty -3 -gapopen 5 -gapextend 2 -query hivreference.fa -db HIVTest -out output.txt 
(sorry about the side scrolling btw)

Now it claims that it cant find the database in the search path, which is odd because if i run the command


blastdbcmd -list db -recursive
It outputs
db\HIVTest Protein

Where Protein is the content type of the database and the HIVTest is the name of the db

My path variables are C:\Dev\blast-2.2.25+\;C:\Dev\blast-2.2.25+\db

So my question is why can blastdb see the db in the db folder ( the path for HIVTest is C:\Dev\blast-2.2.25+\db\ , and there are 3 files a .phr,.pin,.psq)

The cmd line I used to create the database was


makeblastdb -in hiv_sample.fa out ./db/HIVTest

(Note : I converted the original hivsample.fq to hivsample.fa using a perl script I got from http://maq.sourceforge.net/fq_all2std.pl - which isnt a download link, just display and from what I could tell -aka it doesn't die -it works)

To sum up, I'd appreciate any help that you guys could give me regarding this, no rush I just want to know why blastdbcmd can tell me its a database and blastn cant.

Thanks everyone and have a happy new year!

makeblastdb blast blastn • 2.9k views
ADD COMMENTlink modified 7.7 years ago • written 7.7 years ago by Andrewktmeikle0
0
gravatar for Damian Kao
7.7 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

It looks like your db name is 'HIVTest Protein' not just 'HIVTest'. Try

-db 'HIVTest Protein'

in your command

ADD COMMENTlink written 7.7 years ago by Damian Kao15k

That could be it. Spaces in file names are a bad idea, even when the OS allows it.

ADD REPLYlink written 7.7 years ago by Neilfws48k

ah sorry misunderstanding there, there output of that list function is the name of the db and the type of the contents ie its called HIVTest and its a protein db

ADD REPLYlink written 7.7 years ago by Andrewktmeikle0

ah sorry misunderstanding there, the output of that list function is the name of the db and the type of the contents ie its called HIVTest and its a protein db

ADD REPLYlink written 7.7 years ago by Andrewktmeikle0
0
gravatar for Andrewktmeikle
7.6 years ago by
Glasgow
Andrewktmeikle0 wrote:

Turns out I wasnt paying attention, blastn was looking for a nucleotide db where as I was giving it a protein database!

A rather unhelpful if not misleading error received but there you go :P

At least it works now! :D

Thanks for the contributions!

ADD COMMENTlink written 7.6 years ago by Andrewktmeikle0
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