CODEWITHSUNDEEP
python-3.xbioinformatics
A. Navid
A. Navid

Reputation: 21

Error: mdb_env_open: No such file or directory BLAST+ local database problem

So I'm following the NCBI instructions available here: https://www.ncbi.nlm.nih.gov/books/NBK52640/

and I can't for the life of me understand what's wrong here.

Here's my PATH and BLASTDB: path and blastdb

And the error message: Error message

And my blastdb directory: enter image description here

And here's my Python code: 

from Bio.Blast.Applications import NcbipsiblastCommandline
import subprocess


psi_cline = NcbipsiblastCommandline('psiblast', db = 'refseq_protein.00',\
                                        query = "results.fasta", evalue =  10 , \
                                        out = "out_psi.xml", outfmt = 7, \
                                        out_pssm ="pssm-results_pssm")

print(psi_cline)

Upvotes: 0

Views: 5888

Answers (1)

Michael Jarva
Michael Jarva

Reputation: 21

I had this very problem today and it turns out that my blast-database was corrupted in some manner. I recreated my database with makeblastdb and this error went away.

Upvotes: 2

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