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

Question

[langziv]

Hi.

I created a database from a reference genome and I got this error message when I run the blastx command. Earlier today I did the same process for blastn and it was fine.

The entire error message:

BLAST Database error: No alias or index file found for nucleotide database [/index/path] in search path [/current/path:/ncbi-blast/ncbi-blast-2.10.0+/blastdb:/index/path:]

The commands:

Creating the index:

makeblastdb -in "/ncbi_genome.fna" -dbtype prot -parse_seqids -out "/index"

Calling blastsx:

blastn -query "input.fa" -db "reference" -max_hsps 1 -max_target_seqs 50 -num_threads 10 -evalue 1e-5 -out "output.txt"

I'd love to hear your opinions. Thanks.

[GenoMax]

Do you actually have these files right under your / (root) directory? Are you able to write to that location using a standard user account? What does ls -lRh /index* show?

[langziv]

It's not the actual path. I shortened the paths for simplification.

The command you asked about printed the following files:

/.../reference.pdb
/.../reference.phr
/.../reference.pin
/.../reference.pog
/.../reference.pos
/.../reference.pot
/.../reference.psq
/.../reference.ptf
/.../reference.pto

Answer 1

[GenoMax]

blastn -query "input.fa" -db "reference" -max_hsps 1 -max_target_seqs 50 -num_threads 10 -evalue 1e-5 -out "output.txt"

Wait .. that looks like protein database and you are using blastn in your command line. Since you are saying

Calling blastsx:

that must be a typo in command line.

[langziv]

Oh my... you are right. How silly on my behalf. I guess that writing this script in the end of the day might have contributed. Thanks!