-M msa -T raxml fails in OrthoFinder 2.5.5

[wpfeiffer]

Hi,

When testing -M msa -T fasttree, raxml, raxml-ng, and iqtree with -f ExampleData using OrthoFinder 2.5.5, I find that raxml fails, while the other ML codes work. The failure occurs near the end of the analysis with the appended output. I could not find any other “error messages” in the files within Results.

• Do you know what might cause this problem and how it might be resolved?

I installed OrthoFinder on a Linux server using the latest available version of OrthoFinder_source.tar.

Best regards, Wayne

---

Inferring remaining multiple sequence alignments and gene trees

2023-12-19 19:51:19 : Done 0 of 362 2023-12-19 19:51:33 : Done 100 of 362 2023-12-19 19:51:46 : Done 200 of 362 2023-12-19 19:51:56 : Done 300 of 362 ERROR: Species tree inference failed ERROR: An error occurred, please review the error messages they may contain useful information about the problem

[Buckaroo1]

Same problem when using the command on ExampleData: $ orthofinder -M msa -T iqtree -f ExampleData/