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
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!