issue with running Orthofinder

[SrichandanPadhi]

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/

[lauriebelch]

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]

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.

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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 — Reply to this email directly, view it on GitHub <#912 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A6XMJUCUNXEAKVHUTLVPU53ZKTYVFAVCNFSM6AAAAABKJNAKBGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMBYGI3TGMRSGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>