No Support Values

[TT1972]

Hello,
I am running Orthofinder on BUSCO genes of 57 Bakteria.
I am using the following options:

orthofinder -f protein_fasta -S blast -M 'msa' -A 'mafft' -T 'raxml-ng' -a 16

I receive an output with a tree file, but no support values. During the analysis I receive several of these messages:

ERROR: external program called by OrthoFinder returned an error code: 1

Command: raxml-ng --msa /mnt/home/thuenen/Mesorhizobium/protein_fasta/OrthoFinder/Results_Dec06/WorkingDirectory/Alignments_ids/OG0009064.fa --model LG+G4 --seed 12345 --threads 1

stdout:
b'\nRAxML-NG v. 1.2.2 released on 11.04.2024 by The Exelixis Lab.\nDeveloped by: Alexey M. Kozlov and Alexandros Stamatakis.\nContributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth, Julia Haag, Anastasis Togkousidis.\nLatest version: https://github.com/amkozlov/raxml-ng\nQuestions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml\n\nSystem: AMD EPYC 7443 24-Core Processor, 48 cores, 503 GB RAM (allocated: 24 physical cores)\n\nRAxML-NG was called at 08-Dec-2024 07:59:05 as follows:\n\nraxml-ng --msa /mnt/home/thuenen/Mesorhizobium/protein_fasta/OrthoFinder/Results_Dec06/WorkingDirectory/Alignments_ids/OG0009064.fa --model LG+G4 --seed 12345 --threads 1\n\nAnalysis options:\n run mode: ML tree search\n start tree(s): random (10) + parsimony (10)\n random seed: 12345\n tip-inner: OFF\n pattern compression: ON\n per-rate scalers: OFF\n site repeats: ON\n logLH epsilon: general: 10.000000, brlen-triplet: 1000.000000\n fast spr radius: AUTO\n spr subtree cutoff: 1.000000\n fast CLV updates: ON\n branch lengths: proportional (ML estimate, algorithm: NR-FAST)\n SIMD kernels: AVX2\n parallelization: coarse-grained (auto), NONE/sequential\n\n[00:00:00] Reading alignment from file: /mnt/home/thuenen/Mesorhizobium/protein_fasta/OrthoFinder/Results_Dec06/WorkingDirectory/Alignments_ids/OG0009064.fa\n[00:00:00] Loaded alignment with 3 taxa and 42 sites\n\nERROR: Your alignment contains less than 4 sequences! \n\nERROR: Alignment check failed (see details above)!\n\n'
stderr:
b''

Is this the reason I don't get any support values, or am I doing something wrong?

[Jonathan-Holmes-Bioinformatics]

Hi TT1972,

The stdout errors you are receiving is due to OrthoFinder attempting to create trees of Orthogroups containing fewer than 4 sequences. With FastTree as default this isn't a problem but raxml outputs the error you saw and shouldn't have an impact on your output data.

Regarding the lack of support values, The command OrthoFinder uses is, if you want to add bootstrap support you can modify the config.json in the scripts_of folder.

"raxml-ng":{ "program_type": "tree", "cmd_line": "raxml-ng --msa INPUT --model LG+G4 --seed 12345 --threads 1", "ouput_filename": "INPUT.raxml.bestTree" },