Error with diamond

[shelby1245]

Hi David,

I'm trying to run OrthoFinder and I'm getting this error.

ERROR: Cannot run diamond Format of make database command: diamond makedb --in INPUT -d OUTPUT ERROR: Cannot run diamond Format of search database command: diamond blastp -d DATABASE -q INPUT -o OUTPUT --more-sensitive -p 1 --quiet -e 0.001 --compress 1 Please check diamond is installed and that the executables are in the system path

I'm quite new to running code so not too sure how to solve this.

Thanks in advance

[shelby1245]

I've changed the config.json script to the --ignore-warnings and have got diamond 2.0.10 but it now says:

ERROR: Cannot run diamond Format of make database command: diamond makedb --ignore-warnings --in INPUT -d OUTPUT ERROR: Cannot run diamond Format of search database command: diamond blastp --ignore-warnings -d DATABASE -q INPUT -o OUTPUT --more-sensitive -p 1 --quiet -e 0.001 --compress 1 Please check diamond is installed and that the executables are in the system path

[davidemms]

Hi

Have you confirmed that you can run diamond yourself using the command format given in config.json? also, if you've downloaded orthofinder from github then it will look in orthofinder's bin/ directory first for diamond and other executables. If you don't want it to use these then you'll need to delete or move them. Let me know how you get on.

Best wishes David

[lcottret]

Hi,

I think I have the same problem. Orthofinder perfectly works. But when I use a config_orthofinder_user.json to change some parameters of diamond, it fails :

ERROR: Cannot run diamond
Format of make database command:
  diamond makedb --ignore-warnings --in INPUT -d OUTPUT
ERROR: Cannot run diamond
Format of search database command:
  diamond blastp --ignore-warnings -d DATABASE -q INPUT -o OUTPUT --more-sensitive -p 1 --quiet -e 0.001 --compress 1 --id 40
Please check diamond is installed and that the executables are in the system path

Even when I write the full path in the config file, the same error message is returned.

My config_orthofinder_user.json file :

{
     "diamond":{ 
    "program_type": "search",
    "db_cmd": "diamond makedb --ignore-warnings --in INPUT -d OUTPUT",
    "search_cmd": "diamond blastp --ignore-warnings -d DATABASE -q INPUT -o OUTPUT --more-sensitive -p 1 --quiet -e 0.001 --compress 1 --id 40"
    },

    "diamond_ultra_sens":{ 
    "program_type": "search",
    "db_cmd": "diamond makedb --ignore-warnings --in INPUT -d OUTPUT",
    "search_cmd": "diamond blastp --ignore-warnings -d DATABASE -q INPUT -o OUTPUT --ultra-sensitive -p 1 --quiet -e 0.001 --compress 1 --id 40"
    }
        
}

I use the version 2.5.4.

Also, the fact that we have to put a config file in our home directory is not very convenient. Is it possible to put the path of the config file as a parameter in a next release ? This will enable to use different parameters depending on the data that we analyse.

Regards, Ludo

[davidemms]

Hi Ludo

Have you try running the command that OrthoFinder is trying to run?

Best wishes David

[lcottret]

Hi,

Yes the command works.

Ludo