Troubles running blastn against nt database

Question

[ch_at]

Hi there,

I have just started using command line blast. And I have a set of sequences in a .fasta file that I want to run against all the nucleotide (nt) databases that I have downloaded manually from NCBI (nt.00, nt01 ....).

I have put all the nt databases in a folder called "db", where I have Blast installed.

I have tried this command:

blastn -query G1A.fasta -db db/nt.nal -out G1Aoutput.txt

and this one

blastn -query G1A.fasta -db db/nt -out G1Aoutput.txt

and I get this error message:

Command line argument error: Argument "out". File is not accessible:  `G1Aoutput.txt'

I noticed the strange hyphen. Now, I have already looked around and people seemed to have had this problem, when copy-pasting a command. But I typed it myself, no copy and paste involved.

In fact, I have played with Blast around before using my data and I follwed a little tutorial, where I was provided with a query file and a protein database and I was able to create output files just fine...

So curious what might be the problem?

[balasink]

How did you manage to put all the NT databases into db and extract them all? I ran out of room after extracting nt.00, nt.01, and nt.02...and there are 27 parts!

I am so confused...am I only supposed to extract one file and leave the rest as compressed files?

[Adrian Pelin]

nope, you really need to extract them all.

Answer 1

[CikLa]

blastn -query G1A.fasta -db db/nt -out G1Aoutput.txt

Indeed, this command should be Ok. Perhaps permission error prevent you from writing new file.

[ch_at]

Thanks, you were right, I had no permission to write a new file in that folder!