Question: Problem in running OrthoFinder
0
gravatar for mirza
2.2 years ago by
mirza80
India
mirza80 wrote:

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?

blast+ orthofinder • 1.1k views
ADD COMMENTlink modified 12 months ago by david_emms40 • written 2.2 years ago by mirza80

Can you post output of which makeblastdb?

ADD REPLYlink written 2.2 years ago by genomax63k

it returns /usr/bin/makeblastdb :(

ADD REPLYlink written 2.2 years ago by mirza80

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?

ADD REPLYlink written 2.2 years ago by genomax63k

yes, it does get printed.

ADD REPLYlink written 2.2 years ago by mirza80
0
gravatar for david_emms
12 months ago by
david_emms40
david_emms40 wrote:

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
ADD COMMENTlink written 12 months ago by david_emms40
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