I'm trying to make a nucleotide database for my sequences. After opening C:Program Files\NCBI\blast-2.2.28+>
in the command line, I typed in
makeblastdb -in test_gene.fsa -parse_seqids -dbtype nucl
and I got the error message
Building a new db, current time: 07/11/2013 16:07:43
New DB name: test_gene
New DB title: Test_gene
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
BLAST options error: File test_gene does not exist
Then I tried adding the pathway to find the file blast-2.2.28+>makeblastdb -in C:\Program_Files\NCBI\blast-2.2.28+\test_gene.fsa -parse_seqids -dbtype nucl
and I got the same type of error as before. I'm new to this, sorry if this is obvious to fix.
Ok, it works! I used
C:\Program Files\NCBI\blast-2.2.28+>makeblastdb -in test_gene.txt -title test_gene -dbtype nucl -out test_gene
and I got the same stuff as before, but with'Adding sequences from FASTA; added 1 sequence in 0.000725742 seconds.
on the end instead of the error message.Now the only problem is that I don't know where the computer put the database file. I can't find it anywhere. I typed in
C:\Program Files\NCBI\blast-2.2.28+>dir
and the database isn't there. I also made it so i can see hidden and system folders and files, but it isn't there either.Edit: Found it. It was in
C:\Users\Evan\AppData\Local\VirtualStore\Program Files\NCBI\blast-2.2.28+
It's listed under 3 files: test_gene.nhr, test_gene.nin, and test_gene.nsq. I found it usingC:\>dir test_gene* /s /p
in the command line.Perfect. Like I mentioned with the /path/to/blast/databases/..., you have to give the path where you want the database with the -out option.
If this answer solved your problem, don't forget to click on the green check mark next to it to mark it as the correct answer :)