This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Blast 2.2.31+ "makeblastdb": where are my databases?

I'm trying to figure out how to create a local BLAST database from a fasta file with 2000+ sequences. I thought I had it all figured out, but even though the command window says that a database with the correct # of sequences was created, I cannot find my database anywhere on my computer. I feel like I'm going crazy, but it's probably just that I'm not correctly defining the file path where I'd like the database saved? Or am I not actually creating a database? I'm a newby so any advice would be great!

Here's what I've been doing:

C:\Program Files\NCBI\blast-2.2.31+>makeblastdb -in 30B_R1good_phred16Scontigs.f
as -dbtype nucl -out GoodPhred16Scontigs

And here's what I get as an output from the above script:

Building a new DB, current time: 07/06/2015 15:15:40
New DB name:   C:\Program Files\NCBI\blast-2.2.31+\GoodPhred16Scontigs
New DB title:  30B_R1good_phred16Scontigs.fas
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 2232 sequences in 0.504367 seconds.

But there's not actually any type of file created that I can see/find...I'm so confused! Thanks for your help!

blast makeblastdb
• 15,347 views • link
updated by Nanu • Nanu • written by kjojess • kjojess

did you perform a search for the file name on the entire system? check the C:\ and the C:\Program Files\NCBI\blast-2.2.31+ directories specifically

• 0 views • link
updated by Ram Ram • written by steven steven

I've looked everywhere I can think of, but I will check again, thanks!

• 0 views • link
updated by Ram Ram • written by kjojess • kjojess

try running makeblastdb again but this time specify a full path for the output directory

• 0 views • link
written by steven steven

Hello Everyone,

Greetings of the day, I am also facing the problem in windows10, makeblastdb command added the sequences to make database but the output of alias files are not available in bin folder of NCBI/blast. I request you to all please provide me help to get my databases in bin folder.

• 0 views • link
written by Nanu • Nanu

2 answers

It must be in C:\Program Files\NCBI\blast-2.2.31+\GoodPhred16Scontigs

You have to find three new fies starting with the name you selected

• 0 views • link
updated by Ram Ram • written by Antonio R. Franco Antonio R. Franco

That's where I think the files would be as well, but they're nowhere to be found. I'll keep looking though, thanks!

• 0 views • link
written by kjojess • kjojess

The problem was the permissions settings in the directory, thanks for your input!

• 0 views • link
written by kjojess • kjojess

How'd you change the permissions settings?

• 0 views • link
written by sturne29 • sturne29

C:\Program Files\NCBI\blast-2.2.31+>makeblastdb -in <path> -dbtype nucl -out <path>

than you will get new generated files

• 0 views • link
written by Kumar Kumar

This is the script and output when I try to define my file path as you suggested:

​C:\Program Files\NCBI\blast-2.2.31+>makeblastdb -in \C:\Program Files\NCBI\blast
-2.2.31+\30B_R1good_phred16Scontigs.fas -dbtype nucl -out \C:\Program Files\NCBI
\blast-2.2.31+\goodphred
USAGE
  makeblastdb.exe [-h] [-help] [-in input_file] [-input_type type]
    -dbtype molecule_type [-title database_title] [-parse_seqids]
    [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
    [-mask_desc mask_algo_descriptions] [-gi_mask]
    [-gi_mask_name gi_based_mask_names] [-out database_name]
    [-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]
    [-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
   Application to create BLAST databases, version 2.2.31+

Use '-help' to print detailed descriptions of command line arguments
========================================================================

Error: Too many positional arguments (1), the offending value: Files\NCBI\blast-
2.2.31+\30B_R1good_phred16Scontigs.fas

It doesn't like the 'space' in the file path between "Program" and "Files" in "Program Files" but I don't know how to fix it. I must be calling it incorrectly.

The problem might also be with the permissions settings on my directory, trying to change those now...

• 0 views • link
written by kjojess • kjojess

It was a problem with the permissions! Finally got the db files to write. Thanks so much for your help!

• 1 views • link
written by kjojess • kjojess

I have the exactly same problem with you. Could you let me know how you have solved the problem in detail? Thanks in advance.

• 1 views • link
written by t-shouji • t-shouji

Log in to answer this question.

More posts like this