运行动植物泛基因组教程02.gene_family.sh命令如下：
orthofinder.py -f pep \
-S diamond \
-M msa \
-A muscle \
-T fasttree \
-t 10 \
-a 2
报错如下：
Best outgroup(s) for species tree
---------------------------------
2024-11-15 10:50:56 : Starting STRIDE
ERROR: Species tree inference failed
local variable 'speciesTree' referenced before assignment
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.5/scripts_of/__main__.py", line 1790, in main
GetOrthologues(speciesInfoObj, options, prog_caller)
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.5/scripts_of/__main__.py", line 1550, in GetOrthologues
orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse,
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.5/scripts_of/orthologues.py", line 1047, in OrthologuesWorkflow
roots, clusters_counter, rootedSpeciesTreeFN, nSupport, _, _, stride_dups = stride.GetRoot(spTreeFN_ids, files.FileHandler.GetOGsTreeDir(), stride.GeneToSpecies_dash, nHighParallel, qWriteRootedTree=True)
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.5/scripts_of/stride.py", line 513, in GetRoot
species, dict_clades, clade_names = AnalyseSpeciesTree(speciesTree)
Traceback (most recent call last):
File "/share/work/biosoft/OrthoFinder/latest/orthofinder.py", line 7, in <module>
main(args)
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.5/scripts_of/__main__.py", line 1790, in main
GetOrthologues(speciesInfoObj, options, prog_caller)
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.5/scripts_of/__main__.py", line 1550, in GetOrthologues
orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse,
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.5/scripts_of/orthologues.py", line 1047, in OrthologuesWorkflow
roots, clusters_counter, rootedSpeciesTreeFN, nSupport, _, _, stride_dups = stride.GetRoot(spTreeFN_ids, files.FileHandler.GetOGsTreeDir(), stride.GeneToSpecies_dash, nHighParallel, qWriteRootedTree=True)
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.5/scripts_of/stride.py", line 513, in GetRoot
species, dict_clades, clade_names = AnalyseSpeciesTree(speciesTree)
UnboundLocalError: local variable 'speciesTree' referenced before assignment
