ERROR: Species tree inference failed

[dmckeow]

Using OrthoFinder 2.5.5, running it on eukaryotic proteomes, on HPC via Nextflow pipeline.
The following error seems to occur only when certain samples in my dataset are included in the same run - for example two sets of 50 genomes run fine, but when run together this error appears.
It runs with no error on some sets of 50-100 genomes, but others cause this error, and I cannot tell why. I have tried large memory runs (128 GB) on an HPC, and it does not seem to be an out of memory problem.
The syntax warnings at the start of the log appear on successful runs, so I do not think this is the issue.
I'm reallly stumped here - any pointers of how to get to the bottom of this would be really appreciated.
Alternatively, any workaround also appreciated.
Below are two log examples, as you can see they have similar errors:

Log example 1:

/usr/local/bin/scripts_of/tree.py:367: SyntaxWarning: invalid escape sequence '-'
"""
/usr/local/bin/scripts_of/tree.py:1422: SyntaxWarning: invalid escape sequence '-'
"""
/usr/local/bin/scripts_of/newick.py:54: SyntaxWarning: invalid escape sequence '['
_ILEGAL_NEWICK_CHARS = ":;(),[]\t\n\r="
/usr/local/bin/scripts_of/newick.py:57: SyntaxWarning: invalid escape sequence '['
_NHX_RE = "[&&NHX:[^\]]]"
/usr/local/bin/scripts_of/newick.py:58: SyntaxWarning: invalid escape sequence '\d'
_FLOAT_RE = "[+-]?\d+.?\d(?:[eE][-+]\d+)?"
/usr/local/bin/scripts_of/newick.py:60: SyntaxWarning: invalid escape sequence '['
_NAME_RE = "[^():,;\[\]]+"
/usr/local/bin/scripts_of/newick.py:337: SyntaxWarning: invalid escape sequence '\s'
MATCH = '%s\s*%s\s*(%s)?' % (FIRST_MATCH, SECOND_MATCH, _NHX_RE)
/usr/local/bin/scripts_of/probroot.py:10: SyntaxWarning: invalid escape sequence '\i'
"""
/usr/local/bin/scripts_of/probroot.py:201: SyntaxWarning: invalid escape sequence '\l'
"""
/usr/local/bin/scripts_of/probroot.py:267: SyntaxWarning: invalid escape sequence '\l'
"""

OrthoFinder version 2.5.5 Copyright (C) 2014 David Emms

2024-12-05 08:13:29 : Starting OrthoFinder 2.5.5
8 thread(s) for highly parallel tasks (BLAST searches etc.)
2 thread(s) for OrthoFinder algorithm

Checking required programs are installed

Test can run "mcl -h" - ok
Test can run "fastme -i /users/asebe/dmckeown/projects/crg-bcaortho/work/54/f24b6771b150179ba230dda159420b/input/OrthoFinder/Results_orthofinder/WorkingDirectory/dependencies/SimpleTest.phy -o /users/asebe/dmckeown/projects/crg-bcaortho/work/54/f24b6771b150179ba230dda159420b/input/OrthoFinder/Results_orthofinder/WorkingDirectory/dependencies/SimpleTest.tre" - ok

Dividing up work for BLAST for parallel processing

2024-12-05 08:13:29 : Creating diamond database 1 of 19
2024-12-05 08:13:29 : Creating diamond database 2 of 19
2024-12-05 08:13:29 : Creating diamond database 3 of 19
2024-12-05 08:13:29 : Creating diamond database 4 of 19
2024-12-05 08:13:29 : Creating diamond database 5 of 19
2024-12-05 08:13:30 : Creating diamond database 6 of 19
2024-12-05 08:13:30 : Creating diamond database 7 of 19
2024-12-05 08:13:30 : Creating diamond database 8 of 19
2024-12-05 08:13:30 : Creating diamond database 9 of 19
2024-12-05 08:13:30 : Creating diamond database 10 of 19
2024-12-05 08:13:30 : Creating diamond database 11 of 19
2024-12-05 08:13:30 : Creating diamond database 12 of 19
2024-12-05 08:13:30 : Creating diamond database 13 of 19
2024-12-05 08:13:30 : Creating diamond database 14 of 19
2024-12-05 08:13:30 : Creating diamond database 15 of 19
2024-12-05 08:13:30 : Creating diamond database 16 of 19
2024-12-05 08:13:30 : Creating diamond database 17 of 19
2024-12-05 08:13:30 : Creating diamond database 18 of 19
2024-12-05 08:13:30 : Creating diamond database 19 of 19

Running diamond all-versus-all

Using 8 thread(s)
2024-12-05 08:13:30 : This may take some time....
2024-12-05 08:13:30 : Done 0 of 361
2024-12-05 08:13:39 : Done 100 of 361
2024-12-05 08:13:48 : Done 200 of 361
2024-12-05 08:13:58 : Done 300 of 361
2024-12-05 08:14:03 : Done all-versus-all sequence search

Running OrthoFinder algorithm

2024-12-05 08:14:03 : Initial processing of each species
2024-12-05 08:14:03 : Initial processing of species 0 complete
2024-12-05 08:14:03 : Initial processing of species 1 complete
2024-12-05 08:14:03 : Initial processing of species 2 complete
2024-12-05 08:14:04 : Initial processing of species 3 complete
2024-12-05 08:14:04 : Initial processing of species 4 complete
2024-12-05 08:14:04 : Initial processing of species 5 complete
2024-12-05 08:14:04 : Initial processing of species 6 complete
2024-12-05 08:14:04 : Initial processing of species 8 complete
2024-12-05 08:14:04 : Initial processing of species 7 complete
2024-12-05 08:14:05 : Initial processing of species 9 complete
2024-12-05 08:14:05 : Initial processing of species 11 complete
2024-12-05 08:14:05 : Initial processing of species 10 complete
2024-12-05 08:14:05 : Initial processing of species 12 complete
2024-12-05 08:14:05 : Initial processing of species 13 complete
2024-12-05 08:14:05 : Initial processing of species 14 complete
2024-12-05 08:14:05 : Initial processing of species 15 complete
2024-12-05 08:14:06 : Initial processing of species 16 complete
2024-12-05 08:14:06 : Initial processing of species 17 complete
2024-12-05 08:14:06 : Initial processing of species 18 complete
2024-12-05 08:14:09 : Connected putative homologues
2024-12-05 08:14:09 : Written final scores for species 0 to graph file
2024-12-05 08:14:09 : Written final scores for species 3 to graph file
2024-12-05 08:14:09 : Written final scores for species 1 to graph file
2024-12-05 08:14:09 : Written final scores for species 2 to graph file
2024-12-05 08:14:09 : Written final scores for species 4 to graph file
2024-12-05 08:14:09 : Written final scores for species 6 to graph file
2024-12-05 08:14:09 : Written final scores for species 5 to graph file
2024-12-05 08:14:09 : Written final scores for species 7 to graph file
2024-12-05 08:14:09 : Written final scores for species 9 to graph file
2024-12-05 08:14:09 : Written final scores for species 8 to graph file
2024-12-05 08:14:09 : Written final scores for species 12 to graph file
2024-12-05 08:14:09 : Written final scores for species 10 to graph file
2024-12-05 08:14:09 : Written final scores for species 13 to graph file
2024-12-05 08:14:09 : Written final scores for species 11 to graph file
2024-12-05 08:14:09 : Written final scores for species 14 to graph file
2024-12-05 08:14:09 : Written final scores for species 15 to graph file
2024-12-05 08:14:09 : Written final scores for species 16 to graph file
2024-12-05 08:14:09 : Written final scores for species 18 to graph file
2024-12-05 08:14:09 : Written final scores for species 17 to graph file
2024-12-05 08:14:12 : Ran MCL

Writing orthogroups to file

OrthoFinder assigned 2351 genes (97.7% of total) to 82 orthogroups. Fifty percent of all genes were in orthogroups with 132 or more genes (G50 was 132) and were contained in the largest 4 orthogroups (O50 was 4). There were 0 orthogroups with all species present and 0 of these consisted entirely of single-copy genes.

2024-12-05 08:14:12 : Done orthogroups

Analysing Orthogroups

Calculating gene distances

2024-12-05 08:14:17 : Done
/usr/local/lib/python3.12/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
/usr/local/lib/python3.12/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
2024-12-05 08:14:17 : Done 0 of 53
2024-12-05 08:14:17 : Done 10 of 53
2024-12-05 08:14:17 : Done 20 of 53
2024-12-05 08:14:17 : Done 30 of 53
2024-12-05 08:14:17 : Done 40 of 53
Using fallback species tree inference method

Inferring gene and species trees

Best outgroup(s) for species tree

2024-12-05 08:14:20 : Starting STRIDE
File "/usr/local/bin/scripts_of/main.py", line 1790, in main
GetOrthologues(speciesInfoObj, options, prog_caller)
File "/usr/local/bin/scripts_of/main.py", line 1550, in GetOrthologues
orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse,
File "/usr/local/bin/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 "/usr/local/bin/scripts_of/stride.py", line 513, in GetRoot
species, dict_clades, clade_names = AnalyseSpeciesTree(speciesTree)
^^^^^^^^^^^
Traceback (most recent call last):
ERROR: Species tree inference failed
cannot access local variable 'speciesTree' where it is not associated with a value
File "/usr/local/bin/orthofinder", line 7, in
main(args)
File "/usr/local/bin/scripts_of/main.py", line 1790, in main
GetOrthologues(speciesInfoObj, options, prog_caller)
File "/usr/local/bin/scripts_of/main.py", line 1550, in GetOrthologues
orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/bin/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 "/usr/local/bin/scripts_of/stride.py", line 513, in GetRoot
species, dict_clades, clade_names = AnalyseSpeciesTree(speciesTree)
^^^^^^^^^^^
UnboundLocalError: cannot access local variable 'speciesTree' where it is not associated with a value

Log example 2:

/usr/local/bin/scripts_of/tree.py:367: SyntaxWarning: invalid escape sequence '-'
"""
/usr/local/bin/scripts_of/tree.py:1422: SyntaxWarning: invalid escape sequence '-'
"""
/usr/local/bin/scripts_of/newick.py:54: SyntaxWarning: invalid escape sequence '['
_ILEGAL_NEWICK_CHARS = ":;(),[]\t\n\r="
/usr/local/bin/scripts_of/newick.py:57: SyntaxWarning: invalid escape sequence '['
_NHX_RE = "[&&NHX:[^\]]]"
/usr/local/bin/scripts_of/newick.py:58: SyntaxWarning: invalid escape sequence '\d'
_FLOAT_RE = "[+-]?\d+.?\d(?:[eE][-+]\d+)?"
/usr/local/bin/scripts_of/newick.py:60: SyntaxWarning: invalid escape sequence '['
_NAME_RE = "[^():,;\[\]]+"
/usr/local/bin/scripts_of/newick.py:337: SyntaxWarning: invalid escape sequence '\s'
MATCH = '%s\s*%s\s*(%s)?' % (FIRST_MATCH, SECOND_MATCH, _NHX_RE)
/usr/local/bin/scripts_of/probroot.py:10: SyntaxWarning: invalid escape sequence '\i'
"""
/usr/local/bin/scripts_of/probroot.py:201: SyntaxWarning: invalid escape sequence '\l'
"""
/usr/local/bin/scripts_of/probroot.py:267: SyntaxWarning: invalid escape sequence '\l'
"""

OrthoFinder version 2.5.5 Copyright (C) 2014 David Emms

2024-12-05 08:15:48 : Starting OrthoFinder 2.5.5
8 thread(s) for highly parallel tasks (BLAST searches etc.)
2 thread(s) for OrthoFinder algorithm

Checking required programs are installed

Test can run "mcl -h" - ok
Test can run "fastme -i /users/asebe/dmckeown/projects/crg-bcaortho/work/95/84bcd09d04906d600a2b2417c5b0b7/input/OrthoFinder/Results_orthofinder/WorkingDirectory/dependencies/SimpleTest.phy -o /users/asebe/dmckeown/projects/crg-bcaortho/work/95/84bcd09d04906d600a2b2417c5b0b7/input/OrthoFinder/Results_orthofinder/WorkingDirectory/dependencies/SimpleTest.tre" - ok

Dividing up work for BLAST for parallel processing

2024-12-05 08:15:50 : Creating diamond database 1 of 106
2024-12-05 08:15:50 : Creating diamond database 2 of 106
2024-12-05 08:15:50 : Creating diamond database 3 of 106
2024-12-05 08:15:50 : Creating diamond database 4 of 106
2024-12-05 08:15:50 : Creating diamond database 5 of 106
2024-12-05 08:15:50 : Creating diamond database 6 of 106
2024-12-05 08:15:50 : Creating diamond database 7 of 106
2024-12-05 08:15:50 : Creating diamond database 8 of 106
2024-12-05 08:15:50 : Creating diamond database 9 of 106
2024-12-05 08:15:50 : Creating diamond database 10 of 106
2024-12-05 08:15:50 : Creating diamond database 11 of 106
2024-12-05 08:15:50 : Creating diamond database 12 of 106
2024-12-05 08:15:50 : Creating diamond database 13 of 106
2024-12-05 08:15:50 : Creating diamond database 14 of 106
2024-12-05 08:15:50 : Creating diamond database 15 of 106
2024-12-05 08:15:50 : Creating diamond database 16 of 106
2024-12-05 08:15:50 : Creating diamond database 17 of 106
2024-12-05 08:15:50 : Creating diamond database 18 of 106
2024-12-05 08:15:50 : Creating diamond database 19 of 106
2024-12-05 08:15:50 : Creating diamond database 20 of 106
2024-12-05 08:15:50 : Creating diamond database 21 of 106
2024-12-05 08:15:50 : Creating diamond database 22 of 106
2024-12-05 08:15:50 : Creating diamond database 23 of 106
2024-12-05 08:15:50 : Creating diamond database 24 of 106
2024-12-05 08:15:50 : Creating diamond database 25 of 106
2024-12-05 08:15:50 : Creating diamond database 26 of 106
2024-12-05 08:15:50 : Creating diamond database 27 of 106
2024-12-05 08:15:50 : Creating diamond database 28 of 106
2024-12-05 08:15:50 : Creating diamond database 29 of 106
2024-12-05 08:15:50 : Creating diamond database 30 of 106
2024-12-05 08:15:50 : Creating diamond database 31 of 106
2024-12-05 08:15:50 : Creating diamond database 32 of 106
2024-12-05 08:15:50 : Creating diamond database 33 of 106
2024-12-05 08:15:50 : Creating diamond database 34 of 106
2024-12-05 08:15:50 : Creating diamond database 35 of 106
2024-12-05 08:15:50 : Creating diamond database 36 of 106
2024-12-05 08:15:50 : Creating diamond database 37 of 106
2024-12-05 08:15:50 : Creating diamond database 38 of 106
2024-12-05 08:15:51 : Creating diamond database 39 of 106
2024-12-05 08:15:51 : Creating diamond database 40 of 106
2024-12-05 08:15:51 : Creating diamond database 41 of 106
2024-12-05 08:15:51 : Creating diamond database 42 of 106
2024-12-05 08:15:51 : Creating diamond database 43 of 106
2024-12-05 08:15:51 : Creating diamond database 44 of 106
2024-12-05 08:15:51 : Creating diamond database 45 of 106
2024-12-05 08:15:51 : Creating diamond database 46 of 106
2024-12-05 08:15:51 : Creating diamond database 47 of 106
2024-12-05 08:15:51 : Creating diamond database 48 of 106
2024-12-05 08:15:51 : Creating diamond database 49 of 106
2024-12-05 08:15:51 : Creating diamond database 50 of 106
2024-12-05 08:15:51 : Creating diamond database 51 of 106
2024-12-05 08:15:51 : Creating diamond database 52 of 106
2024-12-05 08:15:51 : Creating diamond database 53 of 106
2024-12-05 08:15:51 : Creating diamond database 54 of 106
2024-12-05 08:15:51 : Creating diamond database 55 of 106
2024-12-05 08:15:51 : Creating diamond database 56 of 106
2024-12-05 08:15:51 : Creating diamond database 57 of 106
2024-12-05 08:15:51 : Creating diamond database 58 of 106
2024-12-05 08:15:51 : Creating diamond database 59 of 106
2024-12-05 08:15:51 : Creating diamond database 60 of 106
2024-12-05 08:15:51 : Creating diamond database 61 of 106
2024-12-05 08:15:51 : Creating diamond database 62 of 106
2024-12-05 08:15:51 : Creating diamond database 63 of 106
2024-12-05 08:15:51 : Creating diamond database 64 of 106
2024-12-05 08:15:51 : Creating diamond database 65 of 106
2024-12-05 08:15:51 : Creating diamond database 66 of 106
2024-12-05 08:15:51 : Creating diamond database 67 of 106
2024-12-05 08:15:51 : Creating diamond database 68 of 106
2024-12-05 08:15:51 : Creating diamond database 69 of 106
2024-12-05 08:15:51 : Creating diamond database 70 of 106
2024-12-05 08:15:51 : Creating diamond database 71 of 106
2024-12-05 08:15:51 : Creating diamond database 72 of 106
2024-12-05 08:15:51 : Creating diamond database 73 of 106
2024-12-05 08:15:51 : Creating diamond database 74 of 106
2024-12-05 08:15:51 : Creating diamond database 75 of 106
2024-12-05 08:15:52 : Creating diamond database 76 of 106
2024-12-05 08:15:52 : Creating diamond database 77 of 106
2024-12-05 08:15:52 : Creating diamond database 78 of 106
2024-12-05 08:15:52 : Creating diamond database 79 of 106
2024-12-05 08:15:52 : Creating diamond database 80 of 106
2024-12-05 08:15:52 : Creating diamond database 81 of 106
2024-12-05 08:15:52 : Creating diamond database 82 of 106
2024-12-05 08:15:52 : Creating diamond database 83 of 106
2024-12-05 08:15:52 : Creating diamond database 84 of 106
2024-12-05 08:15:52 : Creating diamond database 85 of 106
2024-12-05 08:15:52 : Creating diamond database 86 of 106
2024-12-05 08:15:52 : Creating diamond database 87 of 106
2024-12-05 08:15:52 : Creating diamond database 88 of 106
2024-12-05 08:15:52 : Creating diamond database 89 of 106
2024-12-05 08:15:52 : Creating diamond database 90 of 106
2024-12-05 08:15:52 : Creating diamond database 91 of 106
2024-12-05 08:15:52 : Creating diamond database 92 of 106
2024-12-05 08:15:52 : Creating diamond database 93 of 106
2024-12-05 08:15:52 : Creating diamond database 94 of 106
2024-12-05 08:15:52 : Creating diamond database 95 of 106
2024-12-05 08:15:52 : Creating diamond database 96 of 106
2024-12-05 08:15:52 : Creating diamond database 97 of 106
2024-12-05 08:15:52 : Creating diamond database 98 of 106
2024-12-05 08:15:52 : Creating diamond database 99 of 106
2024-12-05 08:15:52 : Creating diamond database 100 of 106
2024-12-05 08:15:52 : Creating diamond database 101 of 106
2024-12-05 08:15:52 : Creating diamond database 102 of 106
2024-12-05 08:15:52 : Creating diamond database 103 of 106
2024-12-05 08:15:52 : Creating diamond database 104 of 106
2024-12-05 08:15:52 : Creating diamond database 105 of 106
2024-12-05 08:15:52 : Creating diamond database 106 of 106

Running diamond all-versus-all

Using 8 thread(s)
2024-12-05 08:15:52 : This may take some time....
2024-12-05 08:15:52 : Done 0 of 11236
2024-12-05 08:17:29 : Done 1000 of 11236
2024-12-05 08:18:56 : Done 2000 of 11236
2024-12-05 08:20:23 : Done 3000 of 11236
2024-12-05 08:21:58 : Done 4000 of 11236
2024-12-05 08:23:27 : Done 5000 of 11236
2024-12-05 08:24:58 : Done 6000 of 11236
2024-12-05 08:26:33 : Done 7000 of 11236
2024-12-05 08:28:07 : Done 8000 of 11236
2024-12-05 08:29:34 : Done 9000 of 11236
2024-12-05 08:31:00 : Done 10000 of 11236
2024-12-05 08:32:35 : Done 11000 of 11236
2024-12-05 08:32:55 : Done all-versus-all sequence search

Running OrthoFinder algorithm

2024-12-05 08:32:55 : Initial processing of each species
2024-12-05 08:32:56 : Initial processing of species 0 complete
2024-12-05 08:32:57 : Initial processing of species 1 complete
2024-12-05 08:32:58 : Initial processing of species 2 complete
2024-12-05 08:32:58 : Initial processing of species 3 complete
2024-12-05 08:32:59 : Initial processing of species 4 complete
2024-12-05 08:33:00 : Initial processing of species 5 complete
2024-12-05 08:33:01 : Initial processing of species 6 complete
2024-12-05 08:33:02 : Initial processing of species 7 complete
2024-12-05 08:33:03 : Initial processing of species 8 complete
2024-12-05 08:33:04 : Initial processing of species 9 complete
2024-12-05 08:33:04 : Initial processing of species 10 complete
2024-12-05 08:33:05 : Initial processing of species 11 complete
2024-12-05 08:33:06 : Initial processing of species 12 complete
2024-12-05 08:33:06 : Initial processing of species 13 complete
2024-12-05 08:33:08 : Initial processing of species 14 complete
2024-12-05 08:33:08 : Initial processing of species 15 complete
2024-12-05 08:33:09 : Initial processing of species 16 complete
2024-12-05 08:33:09 : Initial processing of species 17 complete
2024-12-05 08:33:11 : Initial processing of species 18 complete
2024-12-05 08:33:11 : Initial processing of species 19 complete
2024-12-05 08:33:11 : Initial processing of species 20 complete
2024-12-05 08:33:12 : Initial processing of species 21 complete
2024-12-05 08:33:13 : Initial processing of species 22 complete
2024-12-05 08:33:14 : Initial processing of species 23 complete
2024-12-05 08:33:15 : Initial processing of species 24 complete
2024-12-05 08:33:15 : Initial processing of species 25 complete
2024-12-05 08:33:17 : Initial processing of species 27 complete
2024-12-05 08:33:17 : Initial processing of species 26 complete
2024-12-05 08:33:18 : Initial processing of species 29 complete
2024-12-05 08:33:18 : Initial processing of species 28 complete
2024-12-05 08:33:20 : Initial processing of species 31 complete
2024-12-05 08:33:21 : Initial processing of species 32 complete
2024-12-05 08:33:21 : Initial processing of species 30 complete
2024-12-05 08:33:22 : Initial processing of species 34 complete
2024-12-05 08:33:23 : Initial processing of species 33 complete
2024-12-05 08:33:23 : Initial processing of species 35 complete
2024-12-05 08:33:23 : Initial processing of species 36 complete
2024-12-05 08:33:25 : Initial processing of species 37 complete
2024-12-05 08:33:25 : Initial processing of species 38 complete
2024-12-05 08:33:26 : Initial processing of species 40 complete
2024-12-05 08:33:26 : Initial processing of species 39 complete
2024-12-05 08:33:27 : Initial processing of species 41 complete
2024-12-05 08:33:27 : Initial processing of species 42 complete
2024-12-05 08:33:28 : Initial processing of species 43 complete
2024-12-05 08:33:30 : Initial processing of species 44 complete
2024-12-05 08:33:30 : Initial processing of species 45 complete
2024-12-05 08:33:31 : Initial processing of species 46 complete
2024-12-05 08:33:31 : Initial processing of species 47 complete
2024-12-05 08:33:33 : Initial processing of species 49 complete
2024-12-05 08:33:33 : Initial processing of species 48 complete
2024-12-05 08:33:34 : Initial processing of species 51 complete
2024-12-05 08:33:35 : Initial processing of species 50 complete
2024-12-05 08:33:35 : Initial processing of species 52 complete
2024-12-05 08:33:36 : Initial processing of species 53 complete
2024-12-05 08:33:37 : Initial processing of species 54 complete
2024-12-05 08:33:38 : Initial processing of species 55 complete
2024-12-05 08:33:39 : Initial processing of species 57 complete
2024-12-05 08:33:39 : Initial processing of species 56 complete
2024-12-05 08:33:41 : Initial processing of species 58 complete
2024-12-05 08:33:41 : Initial processing of species 59 complete
2024-12-05 08:33:42 : Initial processing of species 60 complete
2024-12-05 08:33:43 : Initial processing of species 61 complete
2024-12-05 08:33:44 : Initial processing of species 63 complete
2024-12-05 08:33:45 : Initial processing of species 62 complete
2024-12-05 08:33:46 : Initial processing of species 64 complete
2024-12-05 08:33:47 : Initial processing of species 65 complete
2024-12-05 08:33:48 : Initial processing of species 66 complete
2024-12-05 08:33:48 : Initial processing of species 67 complete
2024-12-05 08:33:49 : Initial processing of species 68 complete
2024-12-05 08:33:50 : Initial processing of species 69 complete
2024-12-05 08:33:50 : Initial processing of species 70 complete
2024-12-05 08:33:51 : Initial processing of species 72 complete
2024-12-05 08:33:52 : Initial processing of species 71 complete
2024-12-05 08:33:53 : Initial processing of species 73 complete
2024-12-05 08:33:54 : Initial processing of species 74 complete
2024-12-05 08:33:55 : Initial processing of species 76 complete
2024-12-05 08:33:55 : Initial processing of species 75 complete
2024-12-05 08:33:57 : Initial processing of species 77 complete
2024-12-05 08:33:57 : Initial processing of species 78 complete
2024-12-05 08:33:58 : Initial processing of species 80 complete
2024-12-05 08:33:58 : Initial processing of species 79 complete
2024-12-05 08:34:00 : Initial processing of species 81 complete
2024-12-05 08:34:00 : Initial processing of species 82 complete
2024-12-05 08:34:01 : Initial processing of species 83 complete
2024-12-05 08:34:02 : Initial processing of species 84 complete
2024-12-05 08:34:02 : Initial processing of species 85 complete
2024-12-05 08:34:03 : Initial processing of species 86 complete
2024-12-05 08:34:04 : Initial processing of species 88 complete
2024-12-05 08:34:04 : Initial processing of species 87 complete
WARNING: Too few hits between species 90 and species 41 to normalise the scores, these hits will be ignored
2024-12-05 08:34:05 : Initial processing of species 90 complete
2024-12-05 08:34:06 : Initial processing of species 89 complete
2024-12-05 08:34:06 : Initial processing of species 91 complete
2024-12-05 08:34:08 : Initial processing of species 93 complete
2024-12-05 08:34:08 : Initial processing of species 92 complete
2024-12-05 08:34:09 : Initial processing of species 94 complete
2024-12-05 08:34:11 : Initial processing of species 95 complete
2024-12-05 08:34:11 : Initial processing of species 96 complete
2024-12-05 08:34:12 : Initial processing of species 97 complete
2024-12-05 08:34:12 : Initial processing of species 98 complete
2024-12-05 08:34:13 : Initial processing of species 99 complete
2024-12-05 08:34:13 : Initial processing of species 100 complete
2024-12-05 08:34:16 : Initial processing of species 102 complete
2024-12-05 08:34:18 : Initial processing of species 103 complete
2024-12-05 08:34:18 : Initial processing of species 101 complete
2024-12-05 08:34:19 : Initial processing of species 104 complete
2024-12-05 08:34:19 : Initial processing of species 105 complete
2024-12-05 08:34:45 : Connected putative homologues
2024-12-05 08:34:46 : Written final scores for species 0 to graph file
2024-12-05 08:34:46 : Written final scores for species 14 to graph file
2024-12-05 08:34:46 : Written final scores for species 15 to graph file
2024-12-05 08:34:46 : Written final scores for species 1 to graph file
2024-12-05 08:34:46 : Written final scores for species 16 to graph file
2024-12-05 08:34:46 : Written final scores for species 2 to graph file
2024-12-05 08:34:46 : Written final scores for species 17 to graph file
2024-12-05 08:34:46 : Written final scores for species 3 to graph file
2024-12-05 08:34:47 : Written final scores for species 18 to graph file
2024-12-05 08:34:47 : Written final scores for species 4 to graph file
2024-12-05 08:34:47 : Written final scores for species 19 to graph file
2024-12-05 08:34:47 : Written final scores for species 5 to graph file
2024-12-05 08:34:47 : Written final scores for species 20 to graph file
2024-12-05 08:34:47 : Written final scores for species 6 to graph file
2024-12-05 08:34:47 : Written final scores for species 21 to graph file
2024-12-05 08:34:47 : Written final scores for species 7 to graph file
2024-12-05 08:34:47 : Written final scores for species 22 to graph file
2024-12-05 08:34:47 : Written final scores for species 8 to graph file
2024-12-05 08:34:47 : Written final scores for species 23 to graph file
2024-12-05 08:34:48 : Written final scores for species 9 to graph file
2024-12-05 08:34:48 : Written final scores for species 24 to graph file
2024-12-05 08:34:48 : Written final scores for species 10 to graph file
2024-12-05 08:34:48 : Written final scores for species 25 to graph file
2024-12-05 08:34:48 : Written final scores for species 11 to graph file
2024-12-05 08:34:48 : Written final scores for species 26 to graph file
2024-12-05 08:34:48 : Written final scores for species 12 to graph file
2024-12-05 08:34:48 : Written final scores for species 27 to graph file
2024-12-05 08:34:48 : Written final scores for species 13 to graph file
2024-12-05 08:34:49 : Written final scores for species 28 to graph file
2024-12-05 08:34:49 : Written final scores for species 42 to graph file
2024-12-05 08:34:49 : Written final scores for species 43 to graph file
2024-12-05 08:34:49 : Written final scores for species 29 to graph file
2024-12-05 08:34:49 : Written final scores for species 44 to graph file
2024-12-05 08:34:49 : Written final scores for species 30 to graph file
2024-12-05 08:34:49 : Written final scores for species 45 to graph file
2024-12-05 08:34:49 : Written final scores for species 31 to graph file
2024-12-05 08:34:49 : Written final scores for species 32 to graph file
2024-12-05 08:34:49 : Written final scores for species 46 to graph file
2024-12-05 08:34:50 : Written final scores for species 33 to graph file
2024-12-05 08:34:50 : Written final scores for species 47 to graph file
2024-12-05 08:34:50 : Written final scores for species 34 to graph file
2024-12-05 08:34:50 : Written final scores for species 48 to graph file
2024-12-05 08:34:50 : Written final scores for species 35 to graph file
2024-12-05 08:34:50 : Written final scores for species 36 to graph file
2024-12-05 08:34:50 : Written final scores for species 49 to graph file
2024-12-05 08:34:50 : Written final scores for species 37 to graph file
2024-12-05 08:34:50 : Written final scores for species 50 to graph file
2024-12-05 08:34:50 : Written final scores for species 51 to graph file
2024-12-05 08:34:50 : Written final scores for species 38 to graph file
2024-12-05 08:34:50 : Written final scores for species 39 to graph file
2024-12-05 08:34:50 : Written final scores for species 52 to graph file
2024-12-05 08:34:51 : Written final scores for species 40 to graph file
2024-12-05 08:34:51 : Written final scores for species 53 to graph file
2024-12-05 08:34:51 : Written final scores for species 41 to graph file
2024-12-05 08:34:51 : Written final scores for species 54 to graph file
2024-12-05 08:34:51 : Written final scores for species 56 to graph file
2024-12-05 08:34:51 : Written final scores for species 57 to graph file
2024-12-05 08:34:51 : Written final scores for species 55 to graph file
2024-12-05 08:34:51 : Written final scores for species 70 to graph file
2024-12-05 08:34:51 : Written final scores for species 58 to graph file
2024-12-05 08:34:51 : Written final scores for species 71 to graph file
2024-12-05 08:34:51 : Written final scores for species 59 to graph file
2024-12-05 08:34:52 : Written final scores for species 72 to graph file
2024-12-05 08:34:52 : Written final scores for species 60 to graph file
2024-12-05 08:34:52 : Written final scores for species 73 to graph file
2024-12-05 08:34:52 : Written final scores for species 61 to graph file
2024-12-05 08:34:52 : Written final scores for species 74 to graph file
2024-12-05 08:34:52 : Written final scores for species 62 to graph file
2024-12-05 08:34:52 : Written final scores for species 75 to graph file
2024-12-05 08:34:52 : Written final scores for species 63 to graph file
2024-12-05 08:34:52 : Written final scores for species 76 to graph file
2024-12-05 08:34:52 : Written final scores for species 64 to graph file
2024-12-05 08:34:53 : Written final scores for species 77 to graph file
2024-12-05 08:34:53 : Written final scores for species 65 to graph file
2024-12-05 08:34:53 : Written final scores for species 78 to graph file
2024-12-05 08:34:53 : Written final scores for species 66 to graph file
2024-12-05 08:34:53 : Written final scores for species 79 to graph file
2024-12-05 08:34:53 : Written final scores for species 67 to graph file
2024-12-05 08:34:53 : Written final scores for species 80 to graph file
2024-12-05 08:34:53 : Written final scores for species 68 to graph file
2024-12-05 08:34:53 : Written final scores for species 81 to graph file
2024-12-05 08:34:53 : Written final scores for species 69 to graph file
2024-12-05 08:34:53 : Written final scores for species 82 to graph file
2024-12-05 08:34:54 : Written final scores for species 84 to graph file
2024-12-05 08:34:54 : Written final scores for species 83 to graph file
2024-12-05 08:34:54 : Written final scores for species 98 to graph file
2024-12-05 08:34:54 : Written final scores for species 85 to graph file
2024-12-05 08:34:54 : Written final scores for species 86 to graph file
2024-12-05 08:34:54 : Written final scores for species 99 to graph file
2024-12-05 08:34:54 : Written final scores for species 100 to graph file
2024-12-05 08:34:54 : Written final scores for species 87 to graph file
2024-12-05 08:34:54 : Written final scores for species 88 to graph file
2024-12-05 08:34:54 : Written final scores for species 89 to graph file
2024-12-05 08:34:54 : Written final scores for species 101 to graph file
2024-12-05 08:34:54 : Written final scores for species 90 to graph file
2024-12-05 08:34:55 : Written final scores for species 91 to graph file
2024-12-05 08:34:55 : Written final scores for species 102 to graph file
2024-12-05 08:34:55 : Written final scores for species 92 to graph file
2024-12-05 08:34:55 : Written final scores for species 93 to graph file
2024-12-05 08:34:55 : Written final scores for species 103 to graph file
2024-12-05 08:34:55 : Written final scores for species 94 to graph file
2024-12-05 08:34:55 : Written final scores for species 104 to graph file
2024-12-05 08:34:55 : Written final scores for species 105 to graph file
2024-12-05 08:34:55 : Written final scores for species 95 to graph file
2024-12-05 08:34:56 : Written final scores for species 96 to graph file
2024-12-05 08:34:56 : Written final scores for species 97 to graph file

WARNING: program called by OrthoFinder produced output to stderr

Command: mcl /users/asebe/dmckeown/projects/crg-bcaortho/work/95/84bcd09d04906d600a2b2417c5b0b7/input/OrthoFinder/Results_orthofinder/WorkingDirectory/OrthoFinder_graph.txt -I 1.5 -o /users/asebe/dmckeown/projects/crg-bcaortho/work/95/84bcd09d04906d600a2b2417c5b0b7/input/OrthoFinder/Results_orthofinder/WorkingDirectory/clusters_OrthoFinder_I1.5.txt -te 2 -V all

stdout

b''
stderr

b'[mcl] added <2> garbage entries\n'
2024-12-05 08:36:03 : Ran MCL

Writing orthogroups to file

OrthoFinder assigned 10222 genes (99.6% of total) to 92 orthogroups. Fifty percent of all genes were in orthogroups with 2672 or more genes (G50 was 2672) and were contained in the largest 2 orthogroups (O50 was 2). There were 0 orthogroups with all species present and 0 of these consisted entirely of single-copy genes.

2024-12-05 08:36:04 : Done orthogroups

Analysing Orthogroups

Calculating gene distances

2024-12-05 08:37:49 : Done
/usr/local/lib/python3.12/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
/usr/local/lib/python3.12/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
ret = ret.dtype.type(ret / rcount)
2024-12-05 08:37:51 : Done 0 of 54
2024-12-05 08:37:51 : Done 10 of 54
2024-12-05 08:37:51 : Done 20 of 54
2024-12-05 08:37:51 : Done 30 of 54
2024-12-05 08:37:51 : Done 40 of 54
Using fallback species tree inference method

Inferring gene and species trees

Best outgroup(s) for species tree

2024-12-05 08:40:38 : Starting STRIDE
File "/usr/local/bin/scripts_of/main.py", line 1790, in main
GetOrthologues(speciesInfoObj, options, prog_caller)
File "/usr/local/bin/scripts_of/main.py", line 1550, in GetOrthologues
orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse,
File "/usr/local/bin/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 "/usr/local/bin/scripts_of/stride.py", line 513, in GetRoot
species, dict_clades, clade_names = AnalyseSpeciesTree(speciesTree)
^^^^^^^^^^^
ERROR: Species tree inference failed
cannot access local variable 'speciesTree' where it is not associated with a value
Traceback (most recent call last):
File "/usr/local/bin/orthofinder", line 7, in
main(args)
File "/usr/local/bin/scripts_of/main.py", line 1790, in main
GetOrthologues(speciesInfoObj, options, prog_caller)
File "/usr/local/bin/scripts_of/main.py", line 1550, in GetOrthologues
orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/bin/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 "/usr/local/bin/scripts_of/stride.py", line 513, in GetRoot
species, dict_clades, clade_names = AnalyseSpeciesTree(speciesTree)
^^^^^^^^^^^
UnboundLocalError: cannot access local variable 'speciesTree' where it is not associated with a value

[Jonathan-Holmes-Bioinformatics]

Hi dmckeow,

The number of genes in your analysis seems quite low ~50-100. This may be causing STRIDE to fail. Is it possible for you to attach a zip file containing your 20 Proteomes from the example log 1 above so we can have a look and try to reproduce the error.

Thanks