-T raxml-ng——ERROR: Species tree inference failed

[suncimu]

Hello David,

I encountered the following issue while running OrthoFinder: "ERROR: Species tree inference failed." The command I used is: orthofinder -f ./data -t 24 -a 10 -M msa -S diamond -A mafft -T raxml-ng Below is my log file. Could you help me fix it？ Thank you for your assistance. Best regards

2024-05-18 22:41:11 : Creating diamond database 7 of 10 2024-05-18 22:41:11 : Creating diamond database 8 of 10 2024-05-18 22:41:12 : Creating diamond database 9 of 10 2024-05-18 22:41:12 : Creating diamond database 10 of 10

Running diamond all-versus-all

Using 24 thread(s) 2024-05-18 22:41:12 : This may take some time.... 2024-05-18 22:41:12 : Done 0 of 100 2024-05-18 22:43:45 : Done 10 of 100 2024-05-18 22:44:12 : Done 20 of 100 2024-05-18 22:45:44 : Done 30 of 100 2024-05-18 22:46:16 : Done 40 of 100 2024-05-18 22:47:22 : Done 50 of 100 2024-05-18 22:47:49 : Done 60 of 100 2024-05-18 22:48:35 : Done 70 of 100 2024-05-18 22:49:25 : Done all-versus-all sequence search

Running OrthoFinder algorithm

2024-05-18 22:49:25 : Initial processing of each species 2024-05-18 22:49:30 : Initial processing of species 3 complete 2024-05-18 22:49:30 : Initial processing of species 5 complete 2024-05-18 22:49:32 : Initial processing of species 9 complete 2024-05-18 22:49:33 : Initial processing of species 0 complete 2024-05-18 22:49:35 : Initial processing of species 6 complete 2024-05-18 22:49:35 : Initial processing of species 8 complete 2024-05-18 22:49:35 : Initial processing of species 4 complete 2024-05-18 22:49:35 : Initial processing of species 2 complete 2024-05-18 22:49:37 : Initial processing of species 1 complete 2024-05-18 22:49:37 : Initial processing of species 7 complete 2024-05-18 22:49:40 : Connected putative homologues 2024-05-18 22:49:42 : Written final scores for species 3 to graph file 2024-05-18 22:49:42 : Written final scores for species 5 to graph file 2024-05-18 22:49:43 : Written final scores for species 9 to graph file 2024-05-18 22:49:44 : Written final scores for species 0 to graph file 2024-05-18 22:49:44 : Written final scores for species 2 to graph file 2024-05-18 22:49:44 : Written final scores for species 4 to graph file 2024-05-18 22:49:44 : Written final scores for species 6 to graph file 2024-05-18 22:49:44 : Written final scores for species 1 to graph file 2024-05-18 22:49:44 : Written final scores for species 8 to graph file 2024-05-18 22:49:45 : Written final scores for species 7 to graph file 2024-05-18 22:49:53 : Ran MCL

Writing orthogroups to file

OrthoFinder assigned 27399 genes (75.8% of total) to 4887 orthogroups. Fifty percent of all genes were in orthogroups with 5 or more genes (G50 was 5) and were contained in the largest 1600 orthogroups (O50 was 1600). There were 172 orthogroups with all species present and 83 of these consisted entirely of single-copy genes.

2024-05-18 22:49:55 : Done orthogroups

Analysing Orthogroups

2024-05-18 22:49:55 : Starting MSA/Trees Species tree: Using 560 orthogroups with minimum of 60.0% of species having single-copy genes in any orthogroup

Inferring multiple sequence alignments for species tree 2024-05-18 22:49:56 : Done 0 of 560 2024-05-19 00:01:06 : Done 100 of 560 2024-05-19 00:40:48 : Done 200 of 560 2024-05-19 01:16:37 : Done 300 of 560 2024-05-19 01:42:33 : Done 400 of 560 2024-05-19 01:58:23 : Done 500 of 560

Inferring remaining multiple sequence alignments and gene trees 2024-05-19 02:05:09 : Done 0 of 4328 2024-05-20 15:23:20 : Done 1000 of 4328 2024-05-20 16:01:34 : Done 2000 of 4328 2024-05-20 16:04:21 : Done 3000 of 4328 2024-05-20 16:06:49 : Done 4000 of 4328 ERROR: Species tree inference failed ERROR: An error occurred, please review the error messages they may contain useful information about the problem.

[zhanghongbin01]

Hello, I encountered the same problem as you did when using OrthoFinder to construct a species tree with raxml-ng. Could you please share how you eventually solved this issue? Your advice would be greatly appreciated. Thank you very much!

[Buckaroo1]

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

[davidemms]

Hi @suncimu

I think raxml will probably create a log file when inferring the species tree. If this is the case it will be in the WorkingDirectory/alignments directory. Can you see what is reported here?

@Buckaroo1 I think the same will be true with iqtree.

All the best David

[Buckaroo1]

Dear @davidemms

I couldn’t locate the log file you mentioned.

I've attached all the files generated by OrthoFinder: Results_Aug14.zip

Best regards, Buckaroo

[wenxiang-sys]

Same problem when using the command -T raxml，but I succeed when changing to -T fasttree. Hoping for a solution，thank you very much !