Blastn And Blastcmd Issues - Blast

Question

[Andrewktmeikle]

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!

Answer 1

[Damian Kao]

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

-db 'HIVTest Protein'

in your command

[Neilfws]

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

[Andrewktmeikle]

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

[Andrewktmeikle]

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

Answer 2

[Andrewktmeikle]

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!