joao1980
commented
1 year ago Hi, I also obtained this error even after getting the latest version of OrthoFinder. Any updates?
Please find my output below. OrthoFinder version 2.5.5 Copyright (C) 2014 David Emms
2023-07-13 14:12:23 : Starting OrthoFinder 2.5.5 12 thread(s) for highly parallel tasks (BLAST searches etc.) 1 thread(s) for OrthoFinder algorithm
Checking required programs are installed
Test can run "mcl -h" - ok Test can run "fastme -i ./OrtSuite/project/orthofinder_results/Results_Jul13/WorkingDirectory/dependencies/SimpleTest.phy -o ./OrtSuite/project/orthofinder_results/Results_Jul13/WorkingDirectory/dependencies/SimpleTest.tre" - ok
WARNING: Files have been ignored as they don't appear to be FASTA files: info_db.csv info_db.json OrthoFinder expects FASTA files to have one of the following extensions: fas, fa, pep, faa, fasta
Dividing up work for BLAST for parallel processing
2023-07-13 14:12:23 : Creating diamond database 1 of 4 2023-07-13 14:12:23 : Creating diamond database 2 of 4 2023-07-13 14:12:23 : Creating diamond database 3 of 4 2023-07-13 14:12:23 : Creating diamond database 4 of 4
Running diamond all-versus-all
Using 12 thread(s) 2023-07-13 14:12:23 : This may take some time.... 2023-07-13 14:12:23 : Done 0 of 16 2023-07-13 14:12:37 : Done all-versus-all sequence search
Running OrthoFinder algorithm
2023-07-13 14:12:37 : Initial processing of each species WARNING: Too few hits between species 0 and species 1 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 0 and species 2 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 0 and species 3 to normalise the scores, these hits will be ignored 2023-07-13 14:12:37 : Initial processing of species 0 complete WARNING: Too few hits between species 1 and species 0 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 1 and species 2 to normalise the scores, these hits will be ignored 2023-07-13 14:12:37 : Initial processing of species 1 complete WARNING: Too few hits between species 2 and species 0 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 2 and species 1 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 2 and species 3 to normalise the scores, these hits will be ignored 2023-07-13 14:12:37 : Initial processing of species 2 complete WARNING: Too few hits between species 3 and species 0 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 3 and species 2 to normalise the scores, these hits will be ignored 2023-07-13 14:12:37 : Initial processing of species 3 complete 2023-07-13 14:12:39 : Connected putative homologues 2023-07-13 14:12:39 : Written final scores for species 0 to graph file 2023-07-13 14:12:39 : Written final scores for species 1 to graph file 2023-07-13 14:12:39 : Written final scores for species 2 to graph file 2023-07-13 14:12:39 : Written final scores for species 3 to graph file 2023-07-13 14:12:39 : Ran MCL
Writing orthogroups to file
OrthoFinder assigned 1242 genes (88.0% of total) to 63 orthogroups. Fifty percent of all genes were in orthogroups with 58 or more genes (G50 was 58) and were contained in the largest 9 orthogroups (O50 was 9). There were 0 orthogroups with all species present and 0 of these consisted entirely of single-copy genes.
2023-07-13 14:12:39 : Done orthogroups
Analysing Orthogroups
Calculating gene distances
2023-07-13 14:12:42 : Done Using fallback species tree inference method /usr/local/lib/python3.6/site-packages/numpy/core/fromnumeric.py:3373: RuntimeWarning: Mean of empty slice. out=out, **kwargs) /usr/local/lib/python3.6/site-packages/numpy/core/_methods.py:170: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount)
Inferring gene and species trees
2023-07-13 14:12:43 : Done 0 of 40 2023-07-13 14:12:43 : Done 10 of 40 2023-07-13 14:12:43 : Done 20 of 40
Best outgroup(s) for species tree
2023-07-13 14:12:44 : Starting STRIDE
ERROR: Species tree inference failed
local variable 'speciesTree' referenced before assignment
File "/app/OrthoFinder/scripts_of/main.py", line 1790, in main
GetOrthologues(speciesInfoObj, options, prog_caller)
File "/app/OrthoFinder/scripts_of/main.py", line 1569, in GetOrthologues
options.qSplitParaClades)
File "/app/OrthoFinder/scripts_of/orthologues.py", line 1047, in OrthologuesWorkflow
roots, clusterscounter, rootedSpeciesTreeFN, nSupport, , _, stride_dups = stride.GetRoot(spTreeFN_ids, files.FileHandler.GetOGsTreeDir(), stride.GeneToSpecies_dash, nHighParallel, qWriteRootedTree=True)
File "/app/OrthoFinder/scripts_of/stride.py", line 513, in GetRoot
species, dict_clades, clade_names = AnalyseSpeciesTree(speciesTree)
Traceback (most recent call last):
File "./OrthoFinder/orthofinder.py", line 7, in
jmagui
JDuffyEx
Buckaroo1
Hello,
I'm running into an error with v 2.5.5: "ERROR: Species tree inference failed / local variable 'speciesTree' referenced before assignment"
I think this might be a similar error to one previously reported (#782). I tried changing the python version in my conda environment to one earlier than 3.11 (3.10.8) but got the same error.
Any help would be much appreciated. Thanks!
Analysing Orthogroups
Calculating gene distances
2023-06-16 16:09:29 : Done Using fallback species tree inference method /Users/emilytrudeau/miniconda3/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3464: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, /Users/emilytrudeau/miniconda3/lib/python3.10/site-packages/numpy/core/_methods.py:192: RuntimeWarning: invalid value encountered in scalar divide ret = ret.dtype.type(ret / rcount)
Inferring gene and species trees
2023-06-16 16:09:29 : Done 0 of 5
Best outgroup(s) for species tree
2023-06-16 16:09:31 : Starting STRIDE ERROR: Species tree inference failed local variable 'speciesTree' referenced before assignment File "/Users/emilytrudeau/miniconda3/bin/scripts_of/main.py", line 1790, in main GetOrthologues(speciesInfoObj, options, prog_caller) File "/Users/emilytrudeau/miniconda3/bin/scripts_of/main.py", line 1550, in GetOrthologues orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse, File "/Users/emilytrudeau/miniconda3/bin/scripts_of/orthologues.py", line 1047, in OrthologuesWorkflow roots, clusterscounter, rootedSpeciesTreeFN, nSupport, , _, stride_dups = stride.GetRoot(spTreeFN_ids, files.FileHandler.GetOGsTreeDir(), stride.GeneToSpecies_dash, nHighParallel, qWriteRootedTree=True) File "/Users/emilytrudeau/miniconda3/bin/scripts_of/stride.py", line 513, in GetRoot species, dict_clades, clade_names = AnalyseSpeciesTree(speciesTree) Traceback (most recent call last): File "/Users/emilytrudeau/miniconda3/bin/orthofinder", line 7, in
main(args)
File "/Users/emilytrudeau/miniconda3/bin/scripts_of/main.py", line 1790, in main
GetOrthologues(speciesInfoObj, options, prog_caller)
File "/Users/emilytrudeau/miniconda3/bin/scripts_of/main.py", line 1550, in GetOrthologues
orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse,
File "/Users/emilytrudeau/miniconda3/bin/scripts_of/orthologues.py", line 1047, in OrthologuesWorkflow
roots, clusterscounter, rootedSpeciesTreeFN, nSupport, , _, stride_dups = stride.GetRoot(spTreeFN_ids, files.FileHandler.GetOGsTreeDir(), stride.GeneToSpecies_dash, nHighParallel, qWriteRootedTree=True)
File "/Users/emilytrudeau/miniconda3/bin/scripts_of/stride.py", line 513, in GetRoot
species, dict_clades, clade_names = AnalyseSpeciesTree(speciesTree)
UnboundLocalError: local variable 'speciesTree' referenced before assignment