Problem in running OrthoFinder

Question

[mirza]

Hi,

I am trying to run OrthoFinder1.0.7 on my workstation. I have installed orthofinder and all the dependencies including blast+ in my system and added blast+ and blastdb to the path according to the commands given on https://www.ncbi.nlm.nih.gov/books/NBK52640/#_chapter1_Configuration i.e.

$ export PATH=$PATH:$HOME/blast+2.5/bin
export PATH=$PATH:$HOME/bin/blastdb

But when I try to run Orthfinder, it returns the following error,

Checking required programs are installed
-------------------------------------------
Test can run "makeblastdb -help" - failed
ERROR: Cannot run BLAST+

Please check BLAST+ is installed and that the executables are in the system path

Can anyone please help me resolve this problem?

[GenoMax]

Can you post output of which makeblastdb?

[mirza]

it returns /usr/bin/makeblastdb :(

[GenoMax]

Looks like you have another install of blast on your workstation. But makeblastdb -help should have worked. Can you do that and see if help gets printed to screen?

[mirza]

yes, it does get printed.

Answer 1

[david_emms]

Hi

In case this is helpful to anyone else with the same problem: If you've got another version of makeblastdb that is getting used by the system instead of the one you want then just put the directory containing the one you want to use at the start of your PATH variable instead of at the end e.g.

export PATH=$HOME/blast+2.5/bin:$PATH