David Emms

Hi, that's going to be a very challenging task! The computational costs scales at least quadratically, so if you've run a previous analysis on 1000 genomes, for example, then you...

Hi Maria The "full" and "profiles" options should be explained in the paper, basically it's whether you want an orthogroup to be represented by all is members in the diamond...

Hi Nicolas I'm the output I think OrthoFinder should have also printed out the iqtree command it was trying to run. I'd suggest just trying to run that in exactly...

Hi Sorry for the delayed response. This looks like an error in DIAMOND on your machine. Can you try running the command it show (without the --quiet option) and see...

Hi Could you try making a change in ~/anaconda3/envs/orthofinder/bin/scripts_of/config.json that should make the command fail immediately, e.g. "not-diamond blastp -d DATABASE ......." to ensure that the changes you are making...

... in fact, the error message above says the error occurs with diamond makedb, so you will have to make the change to that line to make it work: ```...

Hi Sorry for the delay in answering this, do you see either of these error messages if you use the latest version of OrthoFinder? Best wishes David

Hi, you will probably have the older OrthoFinder in the system path which that command is running. To run an executable that is in your current directory on Linux you...

Hi Natalia It could be that you are using a very old operating system that has an earlier version of GLIBC than 2.25. Try downloading the python source code version...

Hi Could you post the complete output please and I'll have a look. Best wishes David