2026-09-14 17:45:20 : Started OrthoFinder version 3.1.5
Command Line: /opt/env/bin/orthofinder -f proteomes -o of_out -M msa -S diamond -T fasttree -t 128 -a 128

Search program: diamond
MSA program: famsa
Tree program: fasttree
Scoring matrix: BLOSUM62
Gap extend: 1
Gap open: 11

WorkingDirectory_Base: /mnt/SCRATCH/lagr/salmonid_synteny_2026-09/work/2e/b1c1d51e8d2043ff9c85334d639cb7/of_out/Results_Sep14/WorkingDirectory/

Species used: 
0: Ccar.faa
1: Dlab.faa
2: Drer.faa
3: Eluc.faa
4: Gacu.faa
5: Hhuc.faa
6: Hnip.faa
7: Hsap.faa
8: Locu.faa
9: Mmus.faa
10: Nhub.faa
11: Okis.faa
12: Olat.faa
13: Omyk.faa
14: Salp.faa
15: Saur.faa
16: Smax.faa
17: Ssal.faa
18: Stru.faa
19: Tthy.faa
20: Upyg.faa

FN_Orthogroups: /mnt/SCRATCH/lagr/salmonid_synteny_2026-09/work/2e/b1c1d51e8d2043ff9c85334d639cb7/of_out/Results_Sep14/WorkingDirectory/clusters_OrthoFinder_I1.2.txt_id_pairs.txt
WorkingDirectory_Trees: /mnt/SCRATCH/lagr/salmonid_synteny_2026-09/work/2e/b1c1d51e8d2043ff9c85334d639cb7/of_out/Results_Sep14/WorkingDirectory/
2026-09-14 19:10:09 : OrthoFinder run completed