Error when Inferring remaining multiple sequence alignments and gene trees

[marcodimarsico]

Hello there, thank you for this really great tool. Lately, I am trying to perform an orthofinder analysis using 38 species as input, but I am having the following problem.

After the diamond analysis and the analysis of the orthogroups (these process went without any problem), I am having trouble in the part of "Inferring remaining multiple sequence alignments and gene trees". More specific, I got this log:

Inferring remaining multiple sequence alignments and gene trees

2023-06-10 18:11:02 : Done 0 of 30222 File "/home/marco/miniconda3/envs/orthofinder/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/marco/miniconda3/envs/orthofinder/bin/scripts_of/trees_msa.py", line 259, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/marco/miniconda3/envs/orthofinder/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/marco/miniconda3/envs/orthofinder/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")])

Can you give me any suggestion or tell me if there is any possible solution? Thank you very much, I really appreciate it.

[davidemms]

Hi

Was there any more output that was produced? It's hard to see what's gone wrong because there's no error message here, just the line of code where something happened. The logging messages from orthofinder up until this point would also be helpful as they might include some indication of the problem too.

Thanks David