BLAST Database error: No alias or index file found for protein database

Question

[Dracaena]

Hi guys,

I just downloaded a protein fasta file for Arabidopsis which I want to blast my data to. What I did is, I have put the fasta file in a folder, I have used the "makeblastdb" command:

Building a new DB, current time: 11/28/2018 11:21:43
New DB name:   /mnt/d/Primula/Databases/Athaliana/GCF_000001735.4_TAIR10.1_protein
New DB title:  /mnt/d/Primula/Databases/Athaliana/GCF_000001735.4_TAIR10.1_protein.fasta
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 48266 sequences in 2.25262 seconds.*

Both the fasta file and the resulting files are in the same folder. Now, this is my command line I use for the blast:

blastp -query /mypath/genomic.all.maker.proteins.fasta -out PrimVer_actinidia_Arabidopsis.blast.txt -db /pathtofastafolder/GCF_000001735.4_TAIR10.1_protein.fasta -evalue 1e-3 -outfmt 6*

I get this error:

"BLAST Database error: No alias or index file found for protein database"

I refer to the fasta in the -db command, so this is not the problem. Any insights on this?

Cheers

[lieven.sterck]

as it says in your makeblastdb runtime log, the DB name is without .fasta (the DB title is with .fasta apparently)

I usually try to keep these both as much in sync as possible, to avoid confusing as you are experiencing

Answer 1

[Joe]

Try:

blastp -query /mypath/genomic.all.maker.proteins.fasta -out PrimVer_actinidia_Arabidopsis.blast.txt -db /pathtofastafolder/GCF_000001735.4_TAIR10.1_protein -evalue 1e-3 -outfmt 6*

[Dracaena]

This solved it for me! Thanks, altough I don't understand why some people have the opposite problem, i.e. that it does not work withouth adding .fasta.

[Joe]

The problem is that a blast database is made up of several different files. In order to use the database, you have to provide just the stem name, not the extension.

This is equivalent to the DB Name.

Whether or not you need the .fasta extension will depend on whether you set the database name to the input fasta filename when you made the DB.

[Joe]

Great, if this has solved everything, I've moved the comment to an answer now so you can accept it using the tick mark.

[lieven.sterck]

Consider moving it to an answer ;)