Makeblastdb Can'T Find My Fasta Files

Question

[Catie Adair]

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.

Answer 1

[Eric Normandeau]

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?

[Catie Adair]

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.

[Eric Normandeau]

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 :)