Question: Troubles running blastn against nt database
1
gravatar for ch_at
4.8 years ago by
ch_at10
New Zealand
ch_at10 wrote:

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?

blast • 2.1k views
ADD COMMENTlink modified 4.7 years ago by balasink10 • written 4.8 years ago by ch_at10
0
gravatar for CikLa
4.8 years ago by
CikLa90
Malaysia
CikLa90 wrote:
blastn -query G1A.fasta -db db/nt -out G1Aoutput.txt

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

ADD COMMENTlink written 4.8 years ago by CikLa90
0
gravatar for ch_at
4.7 years ago by
ch_at10
New Zealand
ch_at10 wrote:

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

ADD COMMENTlink written 4.7 years ago by ch_at10
0
gravatar for balasink
4.7 years ago by
balasink10
Canada
balasink10 wrote:

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?

 

 

ADD COMMENTlink written 4.7 years ago by balasink10

nope, you really need to extract them all.

ADD REPLYlink written 4.7 years ago by Adrian Pelin2.3k
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