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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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issue with running Orthofinder #912

Open SrichandanPadhi opened 4 days ago

SrichandanPadhi commented 4 days ago

I am getting the following error while running orthofinder. The program runs upto some extent and then displayed error, the error is from speciesTree. Kindly check the below enclosed snapshot.

The command is /home/srichandanp/miniconda3/envs/orthofinder/bin/orthofinder -f /scratch/srichandanp/Genome_Analysis/OrthoFinder_Sequences/

image

lauriebelch commented 3 days ago

Hi SrichandanPadhi,

It seems to have failed to generate a species tree. Can I ask how many species you are analysing, and what kind of species (e.g. plants, bacteria, fungi, a mix)

If possible, it might be worth running orthofinder with your own species tree (using the -s option)

Thanks, Laurie

SrichandanPadhi commented 3 days ago

Hi.. Thank you for your prompt response.

I actually was running on nucleotide sequences with -d as an option. Later I did with the translated sequences, it worked fine and perfectly.

On Thu, Jul 4, 2024 at 12:42 PM lauriebelch @.***> wrote:

Hi SrichandanPadhi,

It seems to have failed to generate a species tree. Can I ask how many species you are analysing, and what kind of species (e.g. plants, bacteria, fungi, a mix)

If possible, it might we worth running orthofinder with your own species tree (using the -s option)

Thanks, Laurie

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