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