Question: Blast 2.2.31+ "makeblastdb": where are my databases?
0
gravatar for kjojess
4.3 years ago by
kjojess0
United States
kjojess0 wrote:

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 • 7.3k views
ADD COMMENTlink modified 2.3 years ago by Nanu0 • written 4.3 years ago by kjojess0

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

ADD REPLYlink written 4.3 years ago by steven70

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

 

ADD REPLYlink written 4.3 years ago by kjojess0

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

ADD REPLYlink written 4.3 years ago by steven70
1
gravatar for Antonio R. Franco
4.3 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.1k wrote:

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

ADD COMMENTlink written 4.3 years ago by Antonio R. Franco4.1k

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

ADD REPLYlink written 4.3 years ago by kjojess0

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

ADD REPLYlink written 4.3 years ago by kjojess0

How'd you change the permissions settings?

ADD REPLYlink written 3.4 years ago by sturne2910
1
gravatar for Manoj
4.3 years ago by
Manoj30
Canada
Manoj30 wrote:

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

than you will get new generated files

ADD COMMENTlink written 4.3 years ago by Manoj30

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...

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by kjojess0

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

ADD REPLYlink written 4.3 years ago by kjojess0

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

ADD REPLYlink written 3.3 years ago by t-shouji0
0
gravatar for Nanu
2.3 years ago by
Nanu0
Nanu0 wrote:

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.

ADD COMMENTlink written 2.3 years ago by Nanu0
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