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davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
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orthofinder3 "assign" option failed #937

Open uguyet opened 4 days ago

uguyet commented 4 days ago

I'm very interested in the new --core and --assign options added to orthofinder3.

I launched orthofinder3 on 1000 genomes with the following command: orthofinder -t 40 -M 'msa' -f input/core/ -o orthofinder_Core

Then I tried to use the "--assign" command to add among 1500 new genomes with the following command: orthofinder --core orthofinder_Core/Results_Nov10/ --assign input/assign -t 40 -a 40 -os -M 'msa'

I got the following error:

40 thread(s) for highly parallel tasks (BLAST searches etc.)
40 thread(s) for OrthoFinder algorithm

INFO: For --assign defaulting to 'mafft --memsave' to reduce RAM usage

INFO: For --assign defaulting to 'FastTree -fastest' to reduce RAM usage

Results directory: /env/export/05_orthofinder_v2/orthofinder_Core/Results_Nov10/../Results_Nov11/

Checking required programs are installed
----------------------------------------
Test can run "astral-pro -i /env/export/05_orthofinder_v2/orthofinder_Core/Results_Nov10/../Results_Nov11/WorkingDirectory/dependencies/astral.input.nwk -o /env/export/05_orthofinder_v2/orthofinder_Core/Results_Nov10/../Results_Nov11/WorkingDirectory/dependencies/astral.output.nwk -t 2" - ok

Creating orthogroup profiles
----------------------------
2024-11-11 12:29:18 : Done 0 of 4905
Sequences must all be the same length

What should I do to correct this problem ? Thanks in advance

lauriebelch commented 3 days ago

orthofinder --core orthofinder_Core/Results_Nov10/ --assign input/assign -t 40 -a 40 -os -M 'msa'

It might be that the path to the --core folder is slightly wrong, try

orthofinder --core orthofinder_Core/OrthoFinder/Results_Nov10/ --assign input/assign -t 40 -a 40 -os -M 'msa'

uguyet commented 3 days ago

Hello, the path to the "core" folder seems good. When I do ls orthofinder_Core/Results_Nov10/, I got the following output:

Citation.txt  Log.txt 
Orthogroups
Orthogroup_Sequences
Orthologues
WorkingDirectory
lauriebelch commented 2 days ago

It looks like core run is maybe still going? It hasn't produced any sequence alignments or gene trees

One thing that might speed it up is using famsa for multiple sequence alignment (instead of mafft). This will become the default in the final release of orthofinder3.

There are some instructions on how to do this in https://github.com/davidemms/OrthoFinder?tab=readme-ov-file#configjson--adding-addtional-programs-for-tree-inference-local-alignment-or-msa