[1802661] Failed to execute script orthofinder

[TonyMannion]

Hello David,

I am trying to run OrthoFinder (version 2.5.4), but after several attempts it fails with same error:

Best outgroup(s) for species tree

2021-07-11 11:15:08 : Starting STRIDE Traceback (most recent call last): File "orthofinder.py", line 7, in File "scripts_of/main.py", line 1801, in main File "scripts_of/main.py", line 1558, in GetOrthologues File "scripts_of/orthologues.py", line 1039, in OrthologuesWorkflow File "scripts_of/stride.py", line 509, in GetRoot File "scripts_of/tree.py", line 221, in init File "scripts_of/newick.py", line 216, in read_newick scripts_of.newick.NewickError: Unexisting tree file or Malformed newick tree structure. [1802661] Failed to execute script orthofinder

In the working directory folder, I see Distance folder (46,116 items in it) and Tree_ids folder (23,057 items in it) as well as SpeciesIDs.txt (8.5kb size) and SpeciesTree_unrooted_ids.txt (0 byte size). Any ideas on if this can be resolved?

Thanks! Tony

[davidemms]

Hi Tony

For some reason the species tree inference has failed. Would you be post the output that OrthoFinder produces which will provide some details and/or email me the WorkingDirectory/SpeciesTrees_ids/ directory to david.emms@plants.ox.ac.uk.

As a temporary workaround you can use the "-M msa" option which will use a different method (multiple sequence alignments) for the species tree inference and so may succeed where this has failed. Once I've got the additional data I can try to fix this issue.

All the best David