I have the error below:

Bio.Application.ApplicationError: Non-zero return code 2 from ‘psiblast -out 7Bio.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::]’NDB_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?

CodePudding user response：

It worked out! The problem was in the way I decompressed the nr file. Previously I used the following command: $ formatdb -i nr.fa -p T

Now I used: $ makeblastdb -in nr.fa -dbtype prot -out nr

Problem solved.