I want to learn how to use NCBI stand alone application but it seems am making a mistake when making a database
Have attached the response i keep getting
(C:\Users\Edwin Wanjofu\OneDrive\BLAST\db>makeblastdb -in Mesorhizobium_Substrain_atpD.fas -dbtype nucl -parse_seqids -ou
t jaribu
Building a new DB, current time: 06/14/2022 18:39:42
New DB name: C:\Users\Edwin Wanjofu\OneDrive\BLAST\db\jaribu
New DB title: Mesorhizobium_Substrain_atpD.fas
Sequence type: Nucleotide
Deleted existing Nucleotide BLAST database named C:\Users\Edwin Wanjofu\OneDrive\BLAST\db\jaribu
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 56 sequences in 0.170692 seconds.
BLAST Database error: No alias or index file found for nucleotide database [C:\Users\Edwin] in search path [C:\Users\Edw
in Wanjofu\OneDrive\BLAST\db;C:\Users\Edwin Wanjofu\OneDrive\BLAST\db;]
Can someone please advise?
The error message is familiar to me. Everything is correct, but when you start a blast search Blast tries to locate your database. It looks for an alias or index file containing the locations of your compiled database, but can't find it. Blast looks first in your home directory or in the working directory for the filename or the alias file that contains the file name. Such alias file must have the names and locations of all the database and the file name must have the extension pal: "your_DB_file(s).pal". See an example of the structure of one of my alias files with the locations of three of my DB files below.
[opperd@big ~]$ cat dippa_all.pal
TITLE D. papillatum proteins and genome
DBLIST "/home/opperd/Proteomes/Euglenozoa/D_papillatum/dippa_translated" "/home/opperd/Proteomes/Euglenozoa/D_papillatum/dippa_longorf_translated" "/home/opperd/Proteomes/Euglenozoa/D_papillatum/dippa"
NSEQ 300000
LENGTH 1000000
The blast package itself also contains a tool to create such files.
Good luck
Fred R. Opperdoes Thanks so much for the response. I think I missed something or I just havent made that file yet. This is what I have in the working directory.
The name of the file you must create should be jaribu.pal and place it in your home directory.
Hope it works
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