BLAST+ error: No alias or index file found for nucleotide database

Question

[Nottuh]

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:

• BLAST Database error: No alias or index file found for nucleotide database
• Why I Am Getting This Error " No Alias Or Index File Found For ..... Database"
• https://stackoverflow.com/questions/26588849/blast-database-error-no-alias-or-index-file-found-for-nucleotide-database

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,...)

[emre.cto]

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

[Nottuh]

That unfortunately didn't do it.

Answer 1

[Tm]

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.

Answer 2

[GenoMax]

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.

[Nottuh]

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

[GenoMax]

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)