2025-08-08 15:00:35 Running OrthoFinder algorithm

2025-08-08 15:00:35 -----------------------------

2025-08-08 15:00:39 2025-08-08 15:00:39 : Initial processing of each species

2025-08-08 15:00:52 2025-08-08 15:00:52 : Initial processing of species 0 complete

2025-08-08 15:00:55 2025-08-08 15:00:55 : Initial processing of species 1 complete

2025-08-08 15:01:10 2025-08-08 15:01:10 : Initial processing of species 2 complete

2025-08-08 15:01:15 2025-08-08 15:01:15 : Initial processing of species 3 complete

2025-08-08 15:01:25 2025-08-08 15:01:25 : Initial processing of species 4 complete

2025-08-08 15:01:38 2025-08-08 15:01:38 : Initial processing of species 5 complete

2025-08-08 15:01:43 2025-08-08 15:01:43 : Initial processing of species 6 complete

2025-08-08 15:01:58 2025-08-08 15:01:58 : Initial processing of species 7 complete

2025-08-08 15:02:07 2025-08-08 15:02:07 : Initial processing of species 8 complete

2025-08-08 15:02:30 2025-08-08 15:02:30 : Initial processing of species 9 complete

2025-08-08 15:02:44 2025-08-08 15:02:44 : Initial processing of species 11 complete

2025-08-08 15:03:13 2025-08-08 15:03:13 : Initial processing of species 12 complete

2025-08-08 15:03:50 2025-08-08 15:03:50 : Initial processing of species 13 complete

2025-08-08 15:03:58 2025-08-08 15:03:58 : Initial processing of species 10 complete

2025-08-08 15:04:03 2025-08-08 15:04:03 : Initial processing of species 14 complete

2025-08-08 15:04:13 2025-08-08 15:04:13 : Initial processing of species 15 complete

2025-08-08 15:04:55 2025-08-08 15:04:55 : Initial processing of species 16 complete

2025-08-08 15:05:56 2025-08-08 15:05:56 : Initial processing of species 17 complete

2025-08-08 15:06:38 2025-08-08 15:06:38 : Connected putative homologues

2025-08-08 15:06:41 2025-08-08 15:06:41 : Written final scores for species 0 to graph file

2025-08-08 15:06:44 2025-08-08 15:06:44 : Written final scores for species 3 to graph file

2025-08-08 15:06:46 2025-08-08 15:06:46 : Written final scores for species 1 to graph file

2025-08-08 15:06:48 2025-08-08 15:06:48 : Written final scores for species 4 to graph file

2025-08-08 15:06:51 2025-08-08 15:06:51 : Written final scores for species 2 to graph file

2025-08-08 15:06:55 2025-08-08 15:06:55 : Written final scores for species 5 to graph file

2025-08-08 15:06:56 2025-08-08 15:06:56 : Written final scores for species 6 to graph file

2025-08-08 15:07:01 2025-08-08 15:07:01 : Written final scores for species 7 to graph file

2025-08-08 15:07:03 2025-08-08 15:07:03 : Written final scores for species 9 to graph file

2025-08-08 15:07:09 2025-08-08 15:07:09 : Written final scores for species 8 to graph file

2025-08-08 15:07:18 2025-08-08 15:07:18 : Written final scores for species 12 to graph file

2025-08-08 15:07:30 2025-08-08 15:07:30 : Written final scores for species 13 to graph file

2025-08-08 15:07:32 2025-08-08 15:07:32 : Written final scores for species 10 to graph file

2025-08-08 15:07:33 2025-08-08 15:07:33 : Written final scores for species 14 to graph file

2025-08-08 15:07:37 2025-08-08 15:07:37 : Written final scores for species 11 to graph file

2025-08-08 15:07:38 2025-08-08 15:07:38 : Written final scores for species 15 to graph file

2025-08-08 15:07:51 2025-08-08 15:07:51 : Written final scores for species 16 to graph file

2025-08-08 15:08:19 2025-08-08 15:08:19 : Written final scores for species 17 to graph file

2025-08-08 15:11:40 2025-08-08 15:11:40 : Ran MCL

2025-08-08 15:11:41 

2025-08-08 15:11:41 Writing orthogroups to file

2025-08-08 15:11:41 ---------------------------

2025-08-08 15:16:25   OrthoFinder assigned 492828 genes (91.8% of total) to 45103 orthogroups. Fifty percent of all genes were in orthogroups with 27 or more genes (G50 was 27) and were contained in the largest 6049 orthogroups (O50 was 6049). There were 2129 orthogroups with all species present and 0 of these consisted entirely of single-copy genes.

2025-08-08 15:16:25 

2025-08-08 15:16:25 2025-08-08 15:16:25 : Done orthogroups

2025-08-08 15:16:25 

2025-08-08 15:16:25 Analysing Orthogroups

2025-08-08 15:16:25 =====================

2025-08-08 15:16:28 2025-08-08 15:16:28 : Starting MSA/Trees

2025-08-08 15:21:09 Species tree: Using 165 orthogroups with minimum of 44.4% of species having single-copy genes in any orthogroup

2025-08-08 15:21:09 

2025-08-08 15:21:09 Inferring multiple sequence alignments for species tree

2025-08-08 15:21:09 -------------------------------------------------------

2025-08-08 15:21:09 2025-08-08 15:21:09 : Done 0 of 165

2025-08-08 15:21:31 2025-08-08 15:21:31 : Done 10 of 165

2025-08-08 15:21:46 2025-08-08 15:21:46 : Done 20 of 165

2025-08-08 15:22:18 2025-08-08 15:22:18 : Done 30 of 165

2025-08-08 15:23:04 2025-08-08 15:23:04 : Done 40 of 165

2025-08-08 15:23:56 2025-08-08 15:23:56 : Done 50 of 165

2025-08-08 15:24:13 2025-08-08 15:24:13 : Done 60 of 165

2025-08-08 15:24:55 2025-08-08 15:24:55 : Done 70 of 165

2025-08-08 15:25:12 2025-08-08 15:25:12 : Done 80 of 165

2025-08-08 15:25:28 2025-08-08 15:25:28 : Done 90 of 165

2025-08-08 15:25:51 2025-08-08 15:25:51 : Done 100 of 165

2025-08-08 15:26:03 2025-08-08 15:26:03 : Done 110 of 165

2025-08-08 15:26:17 2025-08-08 15:26:17 : Done 120 of 165

2025-08-08 15:26:30 2025-08-08 15:26:30 : Done 130 of 165

2025-08-08 15:26:40 2025-08-08 15:26:40 : Done 140 of 165

2025-08-08 15:26:48 2025-08-08 15:26:48 : Done 150 of 165

2025-08-08 15:27:01 

2025-08-08 15:27:01 Inferring remaining multiple sequence alignments and gene trees

2025-08-08 15:27:01 ---------------------------------------------------------------

2025-08-08 15:27:01 2025-08-08 15:27:01 : Done 0 of 44939

2025-08-08 16:26:07 WARNING: 

2025-08-08 16:26:07 list index out of range

2025-08-08 16:26:13   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move

2025-08-08 16:26:13     fn(fns)

2025-08-08 16:26:13   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 262, in trim_fn

2025-08-08 16:26:13     trim.main(fn, fn, 0.1, 500, 0.75)

2025-08-08 16:26:13   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 94, in main

2025-08-08 16:26:13     msa = MSA(infn)

2025-08-08 16:26:13   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 35, in __init__

2025-08-08 16:26:13     self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")])

2025-08-08 16:45:05 WARNING: 

2025-08-08 16:45:05 list index out of range

2025-08-08 16:45:08   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move

2025-08-08 16:45:08     fn(fns)

2025-08-08 16:45:08   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 262, in trim_fn

2025-08-08 16:45:08     trim.main(fn, fn, 0.1, 500, 0.75)

2025-08-08 16:45:08   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 94, in main

2025-08-08 16:45:08     msa = MSA(infn)

2025-08-08 16:45:08   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 35, in __init__

2025-08-08 16:45:08     self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")])

2025-08-08 16:55:55 WARNING: 

2025-08-08 16:55:55 list index out of range

2025-08-08 16:56:06   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move

2025-08-08 16:56:06     fn(fns)

2025-08-08 16:56:06   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 262, in trim_fn

2025-08-08 16:56:06     trim.main(fn, fn, 0.1, 500, 0.75)

2025-08-08 16:56:06   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 94, in main

2025-08-08 16:56:06     msa = MSA(infn)

2025-08-08 16:56:06   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 35, in __init__

2025-08-08 16:56:06     self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")])

2025-08-08 17:11:55 WARNING: 

2025-08-08 17:11:55 list index out of range

2025-08-08 17:35:15 WARNING: 

2025-08-08 17:35:15 list index out of range

2025-08-08 17:35:21   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move

2025-08-08 17:35:21     fn(fns)

2025-08-08 17:35:21   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 262, in trim_fn

2025-08-08 17:35:21     trim.main(fn, fn, 0.1, 500, 0.75)

2025-08-08 17:35:21   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 94, in main

2025-08-08 17:35:21     msa = MSA(infn)

2025-08-08 17:35:21   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 35, in __init__

2025-08-08 17:35:21     self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")])

2025-08-08 17:52:39 WARNING: 

2025-08-08 17:52:39 list index out of range

2025-08-08 17:52:40   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move

2025-08-08 17:52:40     fn(fns)

2025-08-08 17:52:40   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 262, in trim_fn

2025-08-08 17:52:40     trim.main(fn, fn, 0.1, 500, 0.75)

2025-08-08 17:52:40   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 94, in main

2025-08-08 17:52:40     msa = MSA(infn)

2025-08-08 17:52:40   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 35, in __init__

2025-08-08 17:52:40     self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")])

2025-08-08 17:52:50 WARNING: 

2025-08-08 17:52:50 list index out of range

2025-08-08 17:52:51   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move

2025-08-08 17:52:51     fn(fns)

2025-08-08 17:52:51   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 262, in trim_fn

2025-08-08 17:52:51     trim.main(fn, fn, 0.1, 500, 0.75)

2025-08-08 17:52:51   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 94, in main

2025-08-08 17:52:51     msa = MSA(infn)

2025-08-08 17:52:51   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 35, in __init__

2025-08-08 17:52:51     self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")])

2025-08-08 18:40:55 WARNING: 

2025-08-08 18:40:55 list index out of range

2025-08-08 18:48:57 WARNING: 

2025-08-08 18:48:57 list index out of range

2025-08-08 18:49:01   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move

2025-08-08 18:49:01     fn(fns)

2025-08-08 18:49:01   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 262, in trim_fn

2025-08-08 18:49:01     trim.main(fn, fn, 0.1, 500, 0.75)

2025-08-08 18:49:01   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 94, in main

2025-08-08 18:49:01     msa = MSA(infn)

2025-08-08 18:49:01   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 35, in __init__

2025-08-08 18:49:01     self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")])

2025-08-08 19:05:53 WARNING: 

2025-08-08 19:05:53 list index out of range

2025-08-08 19:36:31 WARNING: 

2025-08-08 19:36:31 list index out of range

2025-08-08 19:36:33   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move

2025-08-08 19:36:33     fn(fns)

2025-08-08 19:36:33   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 262, in trim_fn

2025-08-08 19:36:33     trim.main(fn, fn, 0.1, 500, 0.75)

2025-08-08 19:36:33   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 94, in main

2025-08-08 19:36:33     msa = MSA(infn)

2025-08-08 19:36:33   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 35, in __init__

2025-08-08 19:36:33     self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")])

2025-08-08 20:07:14 WARNING: 

2025-08-08 20:07:14 list index out of range

2025-08-08 20:07:14   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move

2025-08-08 20:07:14     fn(fns)

2025-08-08 20:07:14   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 262, in trim_fn

2025-08-08 20:07:14     trim.main(fn, fn, 0.1, 500, 0.75)

2025-08-08 20:07:14   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 94, in main

2025-08-08 20:07:14     msa = MSA(infn)

2025-08-08 20:07:14   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 35, in __init__

2025-08-08 20:07:14     self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")])

2025-08-08 20:19:05 WARNING: 

2025-08-08 20:19:05 list index out of range

2025-08-08 20:19:08   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move

2025-08-08 20:19:08     fn(fns)

2025-08-08 20:19:08   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 262, in trim_fn

2025-08-08 20:19:08     trim.main(fn, fn, 0.1, 500, 0.75)

2025-08-08 20:19:08   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 94, in main

2025-08-08 20:19:08     msa = MSA(infn)

2025-08-08 20:19:08   File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trim.py", line 35, in __init__

2025-08-08 20:19:08     self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")])

2025-08-08 20:58:02 WARNING: 

2025-08-08 20:58:02 list index out of range

2025-08-08 22:19:47 WARNING: 

2025-08-08 22:19:47 list index out of range

2025-08-08 23:19:59 WARNING: 

2025-08-08 23:19:59 list index out of range

2025-08-09 00:21:58 WARNING: 

2025-08-09 00:21:58 list index out of range

2025-08-09 04:18:31 WARNING: 

2025-08-09 04:18:31 list index out of range

2025-08-09 05:05:14 WARNING: 

2025-08-09 05:05:14 list index out of range

2025-08-09 05:13:39 WARNING: 

2025-08-09 05:13:39 list index out of range

2025-08-09 12:45:18 WARNING: 

2025-08-09 12:45:18 list index out of range

2025-08-09 12:45:28 WARNING: 

2025-08-09 12:45:28 list index out of range

2025-08-09 12:49:12 WARNING: 

2025-08-09 12:49:12 list index out of range

2025-08-09 13:51:46 WARNING: 

2025-08-09 13:51:46 list index out of range

2025-08-09 15:08:55 WARNING: 

2025-08-09 15:08:55 list index out of range

2025-08-09 15:36:29 WARNING: 

2025-08-09 15:36:29 list index out of range

2025-08-09 16:14:20 WARNING: 

2025-08-09 16:14:20 list index out of range

2025-08-09 16:19:16 WARNING: 

2025-08-09 16:19:16 list index out of range

2025-08-09 18:24:14 WARNING: 

2025-08-09 18:24:14 list index out of range

2025-08-09 19:23:56   WARNING: 

2025-08-09 19:23:56 list index out of range

2025-08-09 19:35:13 WARNING: 

2025-08-09 19:35:13 list index out of range

2025-08-09 20:32:09 WARNING: 

2025-08-09 20:32:09 list index out of range

2025-08-09 20:38:50 WARNING: 

2025-08-09 20:38:50 list index out of range

2025-08-09 21:31:51 WARNING: 

2025-08-09 21:31:51 list index out of range

2025-08-09 22:53:13 WARNING: 

2025-08-09 22:53:13 list index out of range

2025-08-09 23:39:40 2025-08-09 23:39:38 : Done 1000 of 44939

2025-08-10 00:11:31 WARNING: 

2025-08-10 00:11:31 list index out of range

2025-08-10 00:11:34 WARNING: 

2025-08-10 00:11:34 list index out of range

2025-08-10 01:19:05 WARNING: 

2025-08-10 01:19:05 list index out of range

2025-08-10 01:57:48 WARNING: 

2025-08-10 01:57:48 list index out of range

2025-08-10 02:43:11 WARNING: 

2025-08-10 02:43:11 list index out of range

2025-08-10 02:58:17 WARNING: 

2025-08-10 02:58:17 list index out of range

2025-08-10 04:40:56 WARNING: 

2025-08-10 04:40:56 list index out of range

2025-08-10 04:40:57 WARNING: 

2025-08-10 04:40:57 list index out of range

2025-08-10 05:48:04 2025-08-10 05:48:04 : Done 2000 of 44939

2025-08-10 09:30:46 2025-08-10 09:30:46 : Done 3000 of 44939

2025-08-10 12:05:00 2025-08-10 12:04:59 : Done 4000 of 44939