BLAST Database error in TAXAassign

Question

[Esther Brasil]

Dear all,

I am testing TAXAasign and getting the following error:

[esther@localhost testes]$ ~/Softwares/TAXAassign-master/TAXAassign.sh -t 70 -m 60 -a "60,70,80,95,95,97" -f test.fasta
[2017-05-02 17:10:09] TAXAassign v0.4. Copyright (c) 2013 Computational Microbial Genomics Group, University of Glasgow, UK
[2017-05-02 17:10:09] Using  ~/ncbi-blast-2.6.0+-src/c++/ReleaseMT/bin/blastn
[2017-05-02 17:10:09] Using  ~/Softwares/TAXAassign-master/scripts/blast_concat_taxon.py
[2017-05-02 17:10:09] Using  ~/Softwares/TAXAassign-master/scripts/blast_gen_assignments.pl
[2017-05-02 17:10:09] Blast against NCBI's nt database with minimum percent ident of 60%, maximum of 10 reference sequences, and evalue of 0.0001 in blastn.


BLAST Database error: No alias or index file found for nucleotide database [~ncbi-blast-2.6.0+-src/c++/ReleaseMT/bin/nt] in search path [~/testes::]

I followed all steps here (https://github.com/umerijaz/TAXAassign). When I run update_blastdb.pl nt the tar.gz files are saved at: ncbi-blast-2.6.0+-src/c++/ReleaseMT/bin I created the folder nt inside ncbi/bin and moved the tar.gz files there. I also tried to untar. Not working yet.

Any idea?

Kind regards

Answer 1

[GenoMax]

Have you tried to set BLASTDB variable to the location where the nt files are located?

[Esther Brasil]

Thanks! That solved the problem.