I initially installed the latest OrthoFinder:v3.1.3 using conda into a separate environment, and it ran without any issues. Subsequently, I realized that this version is not compatible with GENESPACE; therefore, I attempted to install the earlier version 2.5.5 using Conda, within a separate environment . However, when I tried to run the analysis it returns some troubles, thought to be related with DIAMOND . Any advice on how to run 2.5.5 version. See print screen below for detailes.
(orthofinder255) konstantin@konstantin-ThinkCentre-M910q:~$ orthofinder -f Data_OF/150426_Tm_Tc_all_non_reg_SP_SPH/
OrthoFinder version 2.5.5 Copyright (C) 2014 David Emms
2026-04-15 16:27:35 : Starting OrthoFinder 2.5.5
4 thread(s) for highly parallel tasks (BLAST searches etc.)
1 thread(s) for OrthoFinder algorithm
Checking required programs are installed
diamond produced the following output:
Error: Invalid option: ignore-warnings
Error: Invalid option: ignore-warnings
ERROR: Cannot run diamond
Environment:
{'SHELL': '/bin/bash', 'SESSION_MANAGER': 'local/konstantin-ThinkCentre-M910q:@/tmp/.ICE-unix/2056,unix/konstantin-ThinkCentre-M910q:/tmp/.ICE-unix/2056', 'WINDOWID': '69206019', 'QT_ACCESSIBILITY': '1', 'COLORTERM': 'truecolor', 'XDG_CONFIG_DIRS': '/etc/xdg/xdg-xubuntu:/etc/xdg', 'XDG_SESSION_PATH': '/org/freedesktop/DisplayManager/Session0', 'XDG_MENU_PREFIX': 'xfce-', 'CONDA_EXE': '/home/konstantin/miniconda3/bin/conda', '_CE_M': '', 'CLUTTER_BACKEND': 'x11', 'GNOME_KEYRING_CONTROL': '/run/user/1000/keyring', 'XDG_CONFIG_HOME': '/home/konstantin/.config', 'DESKTOP_SESSION': 'xubuntu', 'XDG_SEAT': 'seat0', 'PWD': '/home/konstantin', 'LOGNAME': 'konstantin', 'XDG_SESSION_DESKTOP': 'xubuntu', 'QT_QPA_PLATFORMTHEME': 'gtk2', 'XDG_SESSION_TYPE': 'x11', 'CONDA_PREFIX': '/home/konstantin/miniconda3/envs/orthofinder255', 'PANEL_GDK_CORE_DEVICE_EVENTS': '0', 'GPG_AGENT_INFO': '/run/user/1000/gnupg/S.gpg-agent:0:1', 'XAUTHORITY': '/home/konstantin/.Xauthority', 'XDG_GREETER_DATA_DIR': '/var/lib/lightdm/data/konstantin', 'GDM_LANG': 'en_US', 'HOME': '/home/konstantin', 'LANG': 'en_US.UTF-8', 'LS_COLORS': 'rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=00:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arc=01;31:.arj=01;31:.taz=01;31:.lha=01;31:.lz4=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.tzo=01;31:.t7z=01;31:.zip=01;31:.z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.zst=01;31:.tzst=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.alz=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.cab=01;31:.wim=01;31:.swm=01;31:.dwm=01;31:.esd=01;31:.avif=01;35:.jpg=01;35:.jpeg=01;35:.mjpg=01;35:.mjpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.webp=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.oga=00;36:.opus=00;36:.spx=00;36:.xspf=00;36:~=00;90:#=00;90:.bak=00;90:.old=00;90:.orig=00;90:.part=00;90:.rej=00;90:.swp=00;90:.tmp=00;90:.dpkg-dist=00;90:.dpkg-old=00;90:.ucf-dist=00;90:.ucf-new=00;90:.ucf-old=00;90:.rpmnew=00;90:.rpmorig=00;90:.rpmsave=00;90:', 'XDG_CURRENT_DESKTOP': 'XFCE', 'VTE_VERSION': '8003', 'CONDA_PROMPT_MODIFIER': '(orthofinder255) ', 'XDG_SEAT_PATH': '/org/freedesktop/DisplayManager/Seat0', 'XDG_CACHE_HOME': '/home/konstantin/.cache', '_CONDA_EXE': '/home/konstantin/miniconda3/bin/conda', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', '_CONDA_ROOT': '/home/konstantin/miniconda3', 'XDG_SESSION_CLASS': 'user', 'TERM': 'xterm-256color', 'CE_CONDA': '', 'GTK_OVERLAY_SCROLLING': '0', 'LESSOPEN': '| /usr/bin/lesspipe %s', 'USER': 'konstantin', 'CONDA_SHLVL': '2', 'DISPLAY': ':0.0', 'SHLVL': '1', 'XDG_VTNR': '7', 'XDG_SESSION_ID': '2', 'CONDA_PYTHON_EXE': '/home/konstantin/miniconda3/bin/python', 'LD_LIBRARY_PATH': '', 'XDG_RUNTIME_DIR': '/run/user/1000', 'CONDA_DEFAULT_ENV': 'orthofinder255', 'DEBUGINFOD_URLS': 'https://debuginfod.ubuntu.com ', 'XDG_DATA_DIRS': '/usr/share/xubuntu:/usr/share/xfce4:/usr/local/share:/usr/share:/var/lib/snapd/desktop:/usr/share', 'PATH': '/home/konstantin/miniconda3/envs/orthofinder255/bin/scripts_of/bin:/home/konstantin/miniconda3/envs/orthofinder255/bin:/home/konstantin/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin', 'GDMSESSION': 'xubuntu', 'DBUS_SESSION_BUS_ADDRESS': 'unix:path=/run/user/1000/bus', 'CONDA_PREFIX_1': '/home/konstantin/miniconda3', 'CONDA_PREFIX_2': '', '': '/home/konstantin/miniconda3/envs/orthofinder255/bin/orthofinder'}
Command:
export PATH=/home/konstantin/miniconda3/envs/orthofinder255/bin/scripts_of/bin:/home/konstantin/miniconda3/envs/orthofinder255/bin:/home/konstantin/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:
diamond makedb --ignore-warnings --in /home/konstantin/Data_OF/150426_Tm_Tc_all_non_reg_SP_SPH/OrthoFinder/Results_Apr15/WorkingDirectory/dependencies/Species0.fa -d /home/konstantin/Data_OF/150426_Tm_Tc_all_non_reg_SP_SPH/OrthoFinder/Results_Apr15/WorkingDirectory/dependencies/diamondDBSpecies0
diamond blastp --ignore-warnings -d /home/konstantin/Data_OF/150426_Tm_Tc_all_non_reg_SP_SPH/OrthoFinder/Results_Apr15/WorkingDirectory/dependencies/diamondDBSpecies0 -q /home/konstantin/Data_OF/150426_Tm_Tc_all_non_reg_SP_SPH/OrthoFinder/Results_Apr15/WorkingDirectory/dependencies/Species0.fa -o /home/konstantin/Data_OF/150426_Tm_Tc_all_non_reg_SP_SPH/OrthoFinder/Results_Apr15/WorkingDirectory/dependencies/test_search_results.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1
Resolve any issues so that you can successfully run the above commands for OrthoFinder's dependencies on your computer and then re-run OrthoFinder.
Please check diamond is installed and that the executables are in the system path
ERROR: An error occurred, please review the error messages they may contain useful information about the problem.
however, I have diamond installed as shown below.
(base) konstantin@konstantin-ThinkCentre-M910q:$ conda activate orthofinder255
(orthofinder255) konstantin@konstantin-ThinkCentre-M910q:$ diamond help
diamond v0.9.19.120 | by Benjamin Buchfink buchfink@gmail.com
I initially installed the latest OrthoFinder:v3.1.3 using conda into a separate environment, and it ran without any issues. Subsequently, I realized that this version is not compatible with GENESPACE; therefore, I attempted to install the earlier version 2.5.5 using Conda, within a separate environment . However, when I tried to run the analysis it returns some troubles, thought to be related with DIAMOND . Any advice on how to run 2.5.5 version. See print screen below for detailes.
(orthofinder255) konstantin@konstantin-ThinkCentre-M910q:~$ orthofinder -f Data_OF/150426_Tm_Tc_all_non_reg_SP_SPH/
OrthoFinder version 2.5.5 Copyright (C) 2014 David Emms
2026-04-15 16:27:35 : Starting OrthoFinder 2.5.5
4 thread(s) for highly parallel tasks (BLAST searches etc.)
1 thread(s) for OrthoFinder algorithm
Checking required programs are installed
diamond produced the following output:
Error: Invalid option: ignore-warnings
Error: Invalid option: ignore-warnings
ERROR: Cannot run diamond
Environment:
{'SHELL': '/bin/bash', 'SESSION_MANAGER': 'local/konstantin-ThinkCentre-M910q:@/tmp/.ICE-unix/2056,unix/konstantin-ThinkCentre-M910q:/tmp/.ICE-unix/2056', 'WINDOWID': '69206019', 'QT_ACCESSIBILITY': '1', 'COLORTERM': 'truecolor', 'XDG_CONFIG_DIRS': '/etc/xdg/xdg-xubuntu:/etc/xdg', 'XDG_SESSION_PATH': '/org/freedesktop/DisplayManager/Session0', 'XDG_MENU_PREFIX': 'xfce-', 'CONDA_EXE': '/home/konstantin/miniconda3/bin/conda', '_CE_M': '', 'CLUTTER_BACKEND': 'x11', 'GNOME_KEYRING_CONTROL': '/run/user/1000/keyring', 'XDG_CONFIG_HOME': '/home/konstantin/.config', 'DESKTOP_SESSION': 'xubuntu', 'XDG_SEAT': 'seat0', 'PWD': '/home/konstantin', 'LOGNAME': 'konstantin', 'XDG_SESSION_DESKTOP': 'xubuntu', 'QT_QPA_PLATFORMTHEME': 'gtk2', 'XDG_SESSION_TYPE': 'x11', 'CONDA_PREFIX': '/home/konstantin/miniconda3/envs/orthofinder255', 'PANEL_GDK_CORE_DEVICE_EVENTS': '0', 'GPG_AGENT_INFO': '/run/user/1000/gnupg/S.gpg-agent:0:1', 'XAUTHORITY': '/home/konstantin/.Xauthority', 'XDG_GREETER_DATA_DIR': '/var/lib/lightdm/data/konstantin', 'GDM_LANG': 'en_US', 'HOME': '/home/konstantin', 'LANG': 'en_US.UTF-8', 'LS_COLORS': 'rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=00:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arc=01;31:.arj=01;31:.taz=01;31:.lha=01;31:.lz4=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.tzo=01;31:.t7z=01;31:.zip=01;31:.z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.zst=01;31:.tzst=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.alz=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.cab=01;31:.wim=01;31:.swm=01;31:.dwm=01;31:.esd=01;31:.avif=01;35:.jpg=01;35:.jpeg=01;35:.mjpg=01;35:.mjpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.webp=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.oga=00;36:.opus=00;36:.spx=00;36:.xspf=00;36:~=00;90:#=00;90:.bak=00;90:.old=00;90:.orig=00;90:.part=00;90:.rej=00;90:.swp=00;90:.tmp=00;90:.dpkg-dist=00;90:.dpkg-old=00;90:.ucf-dist=00;90:.ucf-new=00;90:.ucf-old=00;90:.rpmnew=00;90:.rpmorig=00;90:.rpmsave=00;90:', 'XDG_CURRENT_DESKTOP': 'XFCE', 'VTE_VERSION': '8003', 'CONDA_PROMPT_MODIFIER': '(orthofinder255) ', 'XDG_SEAT_PATH': '/org/freedesktop/DisplayManager/Seat0', 'XDG_CACHE_HOME': '/home/konstantin/.cache', '_CONDA_EXE': '/home/konstantin/miniconda3/bin/conda', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', '_CONDA_ROOT': '/home/konstantin/miniconda3', 'XDG_SESSION_CLASS': 'user', 'TERM': 'xterm-256color', 'CE_CONDA': '', 'GTK_OVERLAY_SCROLLING': '0', 'LESSOPEN': '| /usr/bin/lesspipe %s', 'USER': 'konstantin', 'CONDA_SHLVL': '2', 'DISPLAY': ':0.0', 'SHLVL': '1', 'XDG_VTNR': '7', 'XDG_SESSION_ID': '2', 'CONDA_PYTHON_EXE': '/home/konstantin/miniconda3/bin/python', 'LD_LIBRARY_PATH': '', 'XDG_RUNTIME_DIR': '/run/user/1000', 'CONDA_DEFAULT_ENV': 'orthofinder255', 'DEBUGINFOD_URLS': 'https://debuginfod.ubuntu.com ', 'XDG_DATA_DIRS': '/usr/share/xubuntu:/usr/share/xfce4:/usr/local/share:/usr/share:/var/lib/snapd/desktop:/usr/share', 'PATH': '/home/konstantin/miniconda3/envs/orthofinder255/bin/scripts_of/bin:/home/konstantin/miniconda3/envs/orthofinder255/bin:/home/konstantin/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin', 'GDMSESSION': 'xubuntu', 'DBUS_SESSION_BUS_ADDRESS': 'unix:path=/run/user/1000/bus', 'CONDA_PREFIX_1': '/home/konstantin/miniconda3', 'CONDA_PREFIX_2': '', '': '/home/konstantin/miniconda3/envs/orthofinder255/bin/orthofinder'}
Command:
export PATH=/home/konstantin/miniconda3/envs/orthofinder255/bin/scripts_of/bin:/home/konstantin/miniconda3/envs/orthofinder255/bin:/home/konstantin/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:
diamond makedb --ignore-warnings --in /home/konstantin/Data_OF/150426_Tm_Tc_all_non_reg_SP_SPH/OrthoFinder/Results_Apr15/WorkingDirectory/dependencies/Species0.fa -d /home/konstantin/Data_OF/150426_Tm_Tc_all_non_reg_SP_SPH/OrthoFinder/Results_Apr15/WorkingDirectory/dependencies/diamondDBSpecies0
diamond blastp --ignore-warnings -d /home/konstantin/Data_OF/150426_Tm_Tc_all_non_reg_SP_SPH/OrthoFinder/Results_Apr15/WorkingDirectory/dependencies/diamondDBSpecies0 -q /home/konstantin/Data_OF/150426_Tm_Tc_all_non_reg_SP_SPH/OrthoFinder/Results_Apr15/WorkingDirectory/dependencies/Species0.fa -o /home/konstantin/Data_OF/150426_Tm_Tc_all_non_reg_SP_SPH/OrthoFinder/Results_Apr15/WorkingDirectory/dependencies/test_search_results.txt --more-sensitive -p 1 --quiet -e 0.001 --compress 1
Resolve any issues so that you can successfully run the above commands for OrthoFinder's dependencies on your computer and then re-run OrthoFinder.
Please check diamond is installed and that the executables are in the system path
ERROR: An error occurred, please review the error messages they may contain useful information about the problem.
however, I have diamond installed as shown below.
(base) konstantin@konstantin-ThinkCentre-M910q:
$ conda activate orthofinder255$ diamond help(orthofinder255) konstantin@konstantin-ThinkCentre-M910q:
diamond v0.9.19.120 | by Benjamin Buchfink buchfink@gmail.com