ERROR: Species tree inference failed

[SHMinger]

When I execute the orthofinder-2.5.5 program，en error was occured. And the outputs are list below, how can i deal with it. anyone can give me a help please?

OrthoFinder version 2.5.5 Copyright (C) 2014 David Emms

2023-07-28 12:45:04 : Starting OrthoFinder 2.5.5 16 thread(s) for highly parallel tasks (BLAST searches etc.) 20 thread(s) for OrthoFinder algorithm

Checking required programs are installed

Test can run "mcl -h" - ok Test can run "mafft" - ok Test can run "raxml" - ok

Dividing up work for BLAST for parallel processing

2023-07-28 12:45:06 : Creating diamond database 1 of 6 2023-07-28 12:45:06 : Creating diamond database 2 of 6 2023-07-28 12:45:06 : Creating diamond database 3 of 6 2023-07-28 12:45:07 : Creating diamond database 4 of 6 2023-07-28 12:45:07 : Creating diamond database 5 of 6 2023-07-28 12:45:07 : Creating diamond database 6 of 6

Running diamond all-versus-all

Using 16 thread(s) 2023-07-28 12:45:07 : This may take some time.... 2023-07-28 12:45:07 : Done 0 of 36 2023-07-28 13:00:04 : Done 10 of 36 2023-07-28 13:04:52 : Done 20 of 36

2023-07-28 13:34:41 : Done all-versus-all sequence search

Running OrthoFinder algorithm

2023-07-28 13:34:42 : Initial processing of each species 2023-07-28 13:34:59 : Initial processing of species 3 complete 2023-07-28 13:34:59 : Initial processing of species 2 complete 2023-07-28 13:35:03 : Initial processing of species 1 complete 2023-07-28 13:35:05 : Initial processing of species 5 complete 2023-07-28 13:35:33 : Initial processing of species 4 complete 2023-07-28 13:36:29 : Initial processing of species 0 complete 2023-07-28 13:36:40 : Connected putative homologues 2023-07-28 13:36:43 : Written final scores for species 3 to graph file 2023-07-28 13:36:43 : Written final scores for species 2 to graph file 2023-07-28 13:36:44 : Written final scores for species 1 to graph file 2023-07-28 13:36:44 : Written final scores for species 5 to graph file 2023-07-28 13:36:47 : Written final scores for species 4 to graph file 2023-07-28 13:36:56 : Written final scores for species 0 to graph file

WARNING: program called by OrthoFinder produced output to stderr

Command: mcl /home/hushuming/data_1/Data_Files/bioinformatics/gene_family/pep/orthofinder_workingdir/OrthoFinder/Results_Jul28/WorkingDirectory/OrthoFinder_graph.txt -I 1.5 -o /home/hushuming/data_1/Data_Files/bioinformatics/gene_family/pep/orthofinder_workingdir/OrthoFinder/Results_Jul28/WorkingDirectory/clusters_OrthoFinder_I1.5.txt -te 20 -V all

stdout

b'' stderr

b'[mcl] cut <55> instances of overlap\n' 2023-07-28 13:37:48 : Ran MCL

Writing orthogroups to file

OrthoFinder assigned 484580 genes (87.6% of total) to 64335 orthogroups. Fifty percent of all genes were in orthogroups with 9 or more genes (G50 was 9) and were contained in the largest 17098 orthogroups (O50 was 17098). There were 14045 orthogroups with all species present and 93 of these consisted entirely of single-copy genes.

2023-07-28 13:37:55 : Done orthogroups

Analysing Orthogroups

2023-07-28 13:37:55 : Starting MSA/Trees Species tree: Using 2749 orthogroups with minimum of 83.3% of species having single-copy genes in any orthogroup

Inferring multiple sequence alignments for species tree

2023-07-28 13:37:59 : Done 0 of 2749 2023-07-28 13:38:08 : Done 1000 of 2749 2023-07-28 13:38:17 : Done 2000 of 2749

Inferring remaining multiple sequence alignments and gene trees

2023-07-28 13:38:25 : Done 0 of 61587 2023-07-28 13:40:45 : Done 1000 of 61587 2023-07-28 13:41:47 : Done 2000 of 61587 2023-07-28 13:42:27 : Done 3000 of 61587 2023-07-28 13:43:01 : Done 4000 of 61587 2023-07-28 13:43:29 : Done 5000 of 61587 2023-07-28 13:43:55 : Done 6000 of 61587 2023-07-28 13:44:16 : Done 7000 of 61587 2023-07-28 13:44:35 : Done 8000 of 61587 2023-07-28 13:44:52 : Done 9000 of 61587 2023-07-28 13:45:09 : Done 10000 of 61587 2023-07-28 13:45:25 : Done 11000 of 61587 2023-07-28 13:45:40 : Done 12000 of 61587 2023-07-28 13:45:53 : Done 13000 of 61587 2023-07-28 13:46:05 : Done 14000 of 61587 2023-07-28 13:46:17 : Done 15000 of 61587 2023-07-28 13:46:30 : Done 16000 of 61587 2023-07-28 13:46:42 : Done 17000 of 61587 2023-07-28 13:46:53 : Done 18000 of 61587 2023-07-28 13:47:06 : Done 19000 of 61587 2023-07-28 13:47:18 : Done 20000 of 61587 2023-07-28 13:47:27 : Done 21000 of 61587 2023-07-28 13:47:37 : Done 22000 of 61587 2023-07-28 13:47:48 : Done 23000 of 61587 2023-07-28 13:47:56 : Done 24000 of 61587 2023-07-28 13:48:04 : Done 25000 of 61587 2023-07-28 13:48:12 : Done 26000 of 61587 2023-07-28 13:48:20 : Done 27000 of 61587 2023-07-28 13:48:28 : Done 28000 of 61587 2023-07-28 13:48:35 : Done 29000 of 61587 2023-07-28 13:48:43 : Done 30000 of 61587 2023-07-28 13:48:50 : Done 31000 of 61587 2023-07-28 13:48:56 : Done 32000 of 61587 2023-07-28 13:49:03 : Done 33000 of 61587 2023-07-28 13:49:10 : Done 34000 of 61587 2023-07-28 13:49:16 : Done 35000 of 61587 2023-07-28 13:49:22 : Done 36000 of 61587 2023-07-28 13:49:28 : Done 37000 of 61587 2023-07-28 13:49:35 : Done 38000 of 61587 2023-07-28 13:49:41 : Done 39000 of 61587 2023-07-28 13:49:47 : Done 40000 of 61587 2023-07-28 13:49:52 : Done 41000 of 61587 2023-07-28 13:49:58 : Done 42000 of 61587 2023-07-28 13:50:04 : Done 43000 of 61587 2023-07-28 13:50:10 : Done 44000 of 61587 2023-07-28 13:50:15 : Done 45000 of 61587 2023-07-28 13:50:21 : Done 46000 of 61587 2023-07-28 13:50:27 : Done 47000 of 61587 2023-07-28 13:50:32 : Done 48000 of 61587 2023-07-28 13:50:37 : Done 49000 of 61587 2023-07-28 13:50:42 : Done 50000 of 61587 2023-07-28 13:50:47 : Done 51000 of 61587 2023-07-28 13:50:52 : Done 52000 of 61587 2023-07-28 13:50:57 : Done 53000 of 61587 2023-07-28 13:51:02 : Done 54000 of 61587 2023-07-28 13:51:07 : Done 55000 of 61587 2023-07-28 13:51:12 : Done 56000 of 61587 2023-07-28 13:51:17 : Done 57000 of 61587 2023-07-28 13:51:22 : Done 58000 of 61587 2023-07-28 13:51:27 : Done 59000 of 61587 2023-07-28 13:51:32 : Done 60000 of 61587 2023-07-28 13:51:37 : Done 61000 of 61587 ERROR: Species tree inference failed ERROR: An error occurred, please review the error messages they may contain useful information about the problem.

[Leavesziqi]

I met the same problem.

[JDuffyEx]

Same problem also. I am running a mixed set of complete and incomplete proteomes of viruses and finding I can only get species tree inference to work by excluding the smaller proteomes. I am wondering if there is a work around for this?

[Buckaroo1]

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