Question: Makeblastdb Can'T Find My Fasta Files
gravatar for Catie Adair
7.2 years ago by
Catie Adair10
Catie Adair10 wrote:

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.

fasta database command-line blast • 4.7k views
ADD COMMENTlink modified 7.2 years ago by Eric Normandeau10k • written 7.2 years ago by Catie Adair10
gravatar for Eric Normandeau
7.2 years ago by
Quebec, Canada
Eric Normandeau10k wrote:

I think the program may be complaining about the output options rather than the input. Notice that the program tells you that test_gene, rather than test_gene.fasta, does not exist.

Here is an example of how I use makeblastdb:

makeblastdb -in contigs.fasta -title contigs_database -dbtype nucl -out /path/to/blast/databases/contigs_database

Note that I use slashes (/) rather than backslashes (\) because I use Linux. On Windows, you will have to substitute them for backslashes, like in your example.

What do you get when you use these options?

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Eric Normandeau10k

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+>dirand 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 using C:\>dir test_gene* /s /p in the command line.

ADD REPLYlink modified 7.2 years ago • written 7.2 years ago by Catie Adair10

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 :)

ADD REPLYlink modified 7.2 years ago • written 7.2 years ago by Eric Normandeau10k
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