Several problems

[abhijeetsingh1704]

There are several problems with orthofinder

1) Docker image problem still existing as of today mon 16 jan 2023 10:56:41 CET docker pull davidemms/orthofinder Using default tag: latest Error response from daemon: manifest for davidemms/orthofinder:latest not found: manifest unknown: manifest unknown

2) conda version is outdated OrthoFinder version 2.4.0 Copyright (C) 2014 David Emms

3) In the latest version -d option is creating problem

• both in docker or local installation Perhaps all the diamond related problems are due to -d option when fna files are used as input. Also, there are problems with orthofinder algorithm when -d option is used, if analysis pass all vs all diamond step

4) Enhancement For the tree construction, Fasttree can be upgraded to Fasttree2 for parallel analysis

[davidemms]

Hi

Thanks for reporting these issues

1) Try docker pull davidemms/orthofinder:2.5.4. I'll take a look into what's happening with the 'latest' tag.

2) OrthoFinder 2.5.4 is available on conda: https://anaconda.org/bioconda/orthofinder

3) Have you got the details, or could you link to the issues if they've already been reported?

4) You can try any tree inference program you would like (including FastTree2) by adding an entry to the config.json file and then choosing that option from the orthofinder command line: https://github.com/davidemms/OrthoFinder#configjson--adding-addtional-programs-for-tree-inference-local-alignment-or-msa. However, the tree inference stage is an embarrassingly parallel task so it is generally better to parallelise over the different trees as OrthoFinder does, rather than running FastTree2 with multiple threads. The second option would likely work out slower.

All the best David