Question: BLAST+ error: No alias or index file found for nucleotide database
0
gravatar for calvin.davey
11 months ago by
calvin.davey10
calvin.davey10 wrote:

Hi, I'm trying to run tblastn, but whatever I try, I always get back the following error:

BLAST Database error: No alias or index file found for nucleotide database [Ptr_protDB] in search path [/home/cadav/Thesis/VanDePeerPSgenes/Shiu_Pipeline/BLAST_output::]

I've looked around the internet for help and found multiple similar answers such as:

But unfortunately, I haven't been able to solve my problem. Though it really shouldn't be that hard... The commands I used were:

makeblastdb -in Ptrichocarpa_210_v3.0.protein.fa -input_type fasta -dbtype 'prot' -title Ptr_protDB -parse_seqids -out Ptr_protDB

Building a new DB, current time: 05/17/2018 13:42:43
New DB name:   /home/cadav/Thesis/VanDePeerPSgenes/Shiu_Pipeline/BLAST_output/Ptr_protDB
New DB title:  Ptr_protDB
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 73013 sequences in 2.85026 seconds.

and

tblastn -db Ptr_protDB -query AnchorPoint/AnchorPoint_masked01.fa -out AP01.blasted -evalue 0.0001 -outfmt 7 -matrix BLOSUM50 -lcase_masking

I've tried using the whole path to the database name, but that unfortunately didn't work. I can't see what I'm doing wrong. Also, why does it does it say: nuclueotide database [Ptr_protDB], even though it's a protein database? I specified it and even created the the 6 files (phr, pin, pog, psd, psi and psq instead of nhr, nin,...)

genome • 1.2k views
ADD COMMENTlink modified 11 months ago by toralmanvar750 • written 11 months ago by calvin.davey10

it should work if you tell blast the full path of the database. you can try the following;

tblastn -db /home/cadav/Thesis/VanDePeerPSgenes/Shiu_Pipeline/BLAST_output/Ptr_protDB -query AnchorPoint/AnchorPoint_masked01.fa -out AP01.blasted -evalue 0.0001 -outfmt 7 -matrix BLOSUM50 -lcase_masking

ADD REPLYlink written 11 months ago by emre.cto0

That unfortunately didn't do it.

ADD REPLYlink written 11 months ago by calvin.davey10
0
gravatar for genomax
11 months ago by
genomax65k
United States
genomax65k wrote:

Set the variable BLASTDB to the directory containing blast indexes like this:

export BLASTDB=/home/cadav/Thesis/VanDePeerPSgenes/Shiu_Pipeline/BLAST_output/

Then try re-running the search.

ADD COMMENTlink modified 11 months ago • written 11 months ago by genomax65k

It didn't work, I still got the same error.

ADD REPLYlink written 11 months ago by calvin.davey10
1

Since you are using tblastn that requires a nucleotide database. You are using a protein one.

Tblastn (search translated nucleotide databases using a protein query) 
Tblastx (Search translated nucleotide databases using a translated nucleotide query)
ADD REPLYlink written 11 months ago by genomax65k
0
gravatar for toralmanvar
11 months ago by
toralmanvar750
toralmanvar750 wrote:

TBLASTN search translated nucleotide databases using a protein query, but in your case I can see that you have prepared protein database using -dbtype 'prot' instead of nucleotide database using 'nucl'. Thus please make sure to use protein sequences as query and database should be nucleotide sequences.

ADD COMMENTlink written 11 months ago by toralmanvar750
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: 1129 users visited in the last hour