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

I have the error below:

Bio.Application.ApplicationError: Non-zero return code 2 from ‘psiblast -out 7NDB_B_WT.out -query 7NDB_B_WT.fasta -db /mnt/research/common-data/Bio/blastdb/nr -evalue 5000 -num_iterations 3 -out_ascii_pssm 7NDB_B_WT.pssm’, message ‘BLAST Database error: No alias or index file found for protein database [/mnt/research/common-data/Bio/blastdb/nr] in search path [/media/leon//Machine_learning_model_binding_free_energy_BFE_change_predictions/TopNetmAb/7NDB/features/7NDB_B_A_344_S::]’

I downloaded the “nr” file from the blast database and created a database link in the directory [/mnt/research/common-data/Bio/blastdb/nr]. But the error persists.

Please, can anyone help me?

Are you working with galaxy or is this just a scripts without any galaxy intentions? This forum is focussed on galaxy related questions so you will get a better answer on more general bioinformatics forums.

The first thing I notice is your sentence:

I downloaded the “nr” file

The nr database consist of many files (Index of /blast/db/v5). How did you downloaded the nr database? Mostly you do it with the tool/command --decompress nr. Also try to execute blast directly from the commandline.

This doubt is not specific to the galaxy. I’m having this problem to apply machine learning to predict binding energy. I’m using every forum I know as I’m desperate to get this sorted out as soon as possible.

I downloaded the nr file contained in the “FASTA” tab.

Thanks for your answer, I will not post more general questions on this forum.

Ah, so you downloaded the 116GB file? You would need to unpack this file (gunzip) and then create a blast database, the basic command is something like makeblastdb -in nr.fa -dbtype prot. But you will be missing things like taxonomic information. See Building a BLAST database with your (local) sequences - BLAST® Command Line Applications User Manual - NCBI Bookshelf
It is highly recommended that you use the --decompress nr command.

You can find this script somewhere in the blast files, sorry dont know on top of my head which folder exactly. Index of /blast/executables/LATEST

1 Like

Yes it is this 116GB file. Thank you for your help @gbbio !