Error in blast+

Question

[Alexis]

Hello, I have a problem with creating a local database (blast+)

I downloaded NCBI BLAST and then put a fasta file in the bin folder. Later I opened this folder in PowerShell and wrote a command makeblastdb -in ownBLASTdb.fasta -out DataBase -dbtype prot -parse_seqids. I got this output:

Building a new DB, current time: 12/03/2023 19:53:12
New DB name:   C:\Program Files\NCBI\blast-2.15.0+\bin\ownBLASTdb.fasta
New DB title:  DataBase
Sequence type: Protein
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 3033 sequences in 0.198722 seconds.


BLAST Database error: No alias or index file found for protein database [C:\Program] in search path [C:\Program Files\NCBI\blast-2.15.0+\bin;;]

What should I do to solve this problem?

And additional question: what path I should write to Environment Variables to use this db with python BLAST?

Answer 1

[Mensur Dlakic]

Joys of doing Bioinformatics on Windows, and consequently dealing with spaces in file and directory names.

I suggest you move your database into a directory/folder that doesn't have a space in its name, so not C:\Program Files\NCBI\blast-2.15.0+\bin. For example, create a folder DB in your C: drive and place the database there. It is not good practice anyway to create database in the same directory where binaries are present. There is probably a more elegant solution, but this should work.

[Shahin]

Spaces are not much better in Linux either. Better never use spaces in naming files, and directories, and column names in SQL Database structures!

[Alexis]

Thanks it works. I appreciate your input.