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?