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

Question

[hrza_mar]

Hi all,

I'm trying to run blastp according to this guide: https://github.com/invertome/crustome

I have downloaded crustome_aa_BLAST.tar.gz and used tar -xvf i got following files: crustome_aa.00.phr crustome_aa.00.pin crustome_aa.00.pog crustome_aa.00.psd crustome_aa.00.psi crustome_aa.00.psq crustome_aa.01.phr crustome_aa.01.pin crustome_aa.01.pog crustome_aa.01.psd crustome_aa.01.psi crustome_aa.01.psq crustome_aa.02.phr crustome_aa.02.pin crustome_aa.02.pog crustome_aa.02.psd crustome_aa.02.psi crustome_aa.02.psq crustome_aa.pal dict

and they are all in crustome_aa_DB director in my working directory but when I run :

blastp -query reference.fasta -db crustome_aa_DB -num_threads 5 -max_target_seqs 1000 -evalue 1e-96 -outfmt "6 qseqid sseqid evalue bitscore pident nident qlen slen qstart qend sstart send length mismatch gapopen" -out hits.tsv

I get: BLAST Database error: No alias or index file found for protein database [crustome_aa_DB] in search path

I have also triend with nr database for testing out the problem, downloaded with

update_blastdb.pl --decompress nr [*]

Same problem.

Does anyone know what exactly is the problem? I have tried with export BLASTDB= and point to the database but to no success

Thanks

Answer 1

[Mensur Dlakic]

Not sure why you are typing crustome_aa_DB as a database name when your file names are completely different. You should use whatever the common name is for all those files up to the first dot. So:

-db crustome_aa_DB/crustome_aa

[hrza_mar]

Ok thanks it worked.

I did export BLASTDB=/home/ubuntu/crustome_aa

blastp -query reference.fasta -db crustome_aa ...