Question: Error with database alias when running blastp
0
gravatar for thjnant
5.0 years ago by
thjnant90
Germany
thjnant90 wrote:

I have made a blast protein database with this command:

./makeblastdb -in input.fsa -out prot.db -dbtype prot -hash_index

It has generated 8 files as follows:

prot.db.phd  prot.db.phi  prot.db.phr  prot.db.pin  prot.db.pog  prot.db.psd  prot.db.psi  prot.db.psq

I have put everything in one folder called prot.db and now want to run the blastp with this command:

blastp -db  prot.db/ -query pep.fa -out results.out

But it gives me the following error which I don't understand how to solve:
BLAST Database error: No alias or index file found for protein database [prot.db/] in search path

I have been looking around to find a solution but I don't understand how I should proceed. Any help would be appreciated.

 

blast • 1.6k views
ADD COMMENTlink modified 5.0 years ago by Pierre Lindenbaum123k • written 5.0 years ago by thjnant90

The error indicates the file stated in your -db is not a database file or it cannot find it. Therefore, make sure it was made into a BLASTable database by running makeblastdb -in filename -dbtype databasetype -out outputfile

 

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by smlail.umuc0
0
gravatar for Pierre Lindenbaum
5.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

use `prot.db` , not `prot.db/`

ADD COMMENTlink written 5.0 years ago by Pierre Lindenbaum123k

Unfortunately, I still get the same error.

ADD REPLYlink written 5.0 years ago by thjnant90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2058 users visited in the last hour