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.
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 update_blastdb.pl --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.