OrthoFinder
OrthoFinder copied to clipboard
davidemms
Version 2.5.4 NewickError Unexisting tree file but I can find tree file
I ran Orthofinder.
Best outgroup(s) for species tree
2022-11-28 16:11:52 : Starting STRIDE Traceback (most recent call last): File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/stride.py", line 506, in GetRoot speciesTree = tree.Tree(speciesTreeFN, format=2) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/tree.py", line 221, in init read_newick(newick, root_node = self, format=format) File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/newick.py", line 216, in read_newick raise NewickError('Unexisting tree file or Malformed newick tree structure.') scripts_of.newick.NewickError: Unexisting tree file or Malformed newick tree structure.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/olivia/anaconda3/envs/orthofinder_source/bin/orthofinder", line 7, in
NOTE: I found tree_id.txt at .../Results_Nov29/WorkingDirectory/Tree_ids/
Please advice! Thank you!
Hi
I think you might be running an old version and this issue has been fixed in the latest version (2.5.4).
All the best David
Dear David,
I am running version 2.5.4 and this problem still occurs.
Please advice.
Thank you.
Regards, Olivia
From: David Emms @.> Sent: Tuesday, November 29, 2022 4:44 PM To: davidemms/OrthoFinder @.> Cc: #OLIVIA AGATHA# @.>; Author @.> Subject: Re: [davidemms/OrthoFinder] NewickError Unexisting tree file but I can find tree file (Issue #768)
Hi
I think you might be running an old version and this issue has been fixed in the latest version (2.5.4).
All the best David
— Reply to this email directly, view it on GitHubhttps://github.com/davidemms/OrthoFinder/issues/768#issuecomment-1330280309, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A4O6KPHHGE44YXALCSBHGZTWKW66XANCNFSM6AAAAAASOEWQGA. You are receiving this because you authored the thread.Message ID: @.***>
Hi Olivia
Could you paste the full log from the start of the run please, it may contain a clue as to what caused the problem.
All the best David
Hi @biology-han
I've deleted your message as it is not relevant to this issue. If you have an issue could you please post it as a new issue and provide a full description of the problem, the information you've put here doesn't explain to me what the issue is that you have found.
Best wishes David
OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms
2022-11-29 17:22:03 : Starting OrthoFinder 2.5.4 128 thread(s) for highly parallel tasks (BLAST searches etc.) 16 thread(s) for OrthoFinder algorithm
Checking required programs are installed
Test can run "mcl -h" - ok Test can run "fastme -i /home/olivia/OrthoFinder_source/Proteomes_SL/primary_transcripts/OrthoFinder/Results_Nov29_1/WorkingDirectory/SimpleTest.phy -o /home/olivia/OrthoFinder_source/Proteomes_SL/primary_transcripts/OrthoFinder/Results_Nov29_1/WorkingDirectory/SimpleTest.tre" - ok
Dividing up work for BLAST for parallel processing
2022-11-29 17:22:05 : Creating diamond database 1 of 12 2022-11-29 17:22:05 : Creating diamond database 2 of 12 2022-11-29 17:22:06 : Creating diamond database 3 of 12 2022-11-29 17:22:06 : Creating diamond database 4 of 12 2022-11-29 17:22:06 : Creating diamond database 5 of 12 2022-11-29 17:22:06 : Creating diamond database 6 of 12 2022-11-29 17:22:07 : Creating diamond database 7 of 12 2022-11-29 17:22:07 : Creating diamond database 8 of 12 2022-11-29 17:22:07 : Creating diamond database 9 of 12 2022-11-29 17:22:07 : Creating diamond database 10 of 12 2022-11-29 17:22:07 : Creating diamond database 11 of 12 2022-11-29 17:22:07 : Creating diamond database 12 of 12
Running diamond all-versus-all
Using 128 thread(s) 2022-11-29 17:22:08 : This may take some time.... 2022-11-29 17:22:10 : Done 0 of 144 2022-11-29 17:22:10 : Done 10 of 144 2022-11-29 18:40:22 : Done all-versus-all sequence search
Running OrthoFinder algorithm
2022-11-29 18:40:23 : Initial processing of each species WARNING: Too few hits between species 2 and species 3 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 WARNING: Too few hits between species 3 and species 3 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 2 and species 7 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 3 and species 7 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 7 and species 2 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 7 and species 3 to normalise the scores, these hits will be ignored 2022-11-29 18:40:23 : Initial processing of species 2 complete 2022-11-29 18:40:23 : Initial processing of species 0 complete WARNING: Too few hits between species 3 and species 10 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 7 and species 7 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 10 and species 3 to normalise the scores, these hits will be ignored WARNING: Too few hits between species 7 and species 10 to normalise the scores, these hits will be ignored 2022-11-29 18:40:24 : Initial processing of species 3 complete 2022-11-29 18:40:24 : Initial processing of species 6 complete WARNING: Too few hits between species 10 and species 7 to normalise the scores, these hits will be ignored 2022-11-29 18:40:24 : Initial processing of species 7 complete 2022-11-29 18:40:24 : Initial processing of species 9 complete 2022-11-29 18:40:24 : Initial processing of species 10 complete 2022-11-29 18:41:26 : Initial processing of species 8 complete 2022-11-29 18:41:34 : Initial processing of species 5 complete 2022-11-29 18:42:01 : Initial processing of species 4 complete 2022-11-29 18:42:25 : Initial processing of species 1 complete 2022-11-29 18:42:55 : Initial processing of species 11 complete 2022-11-29 18:43:12 : Connected putative homologues 2022-11-29 18:43:12 : Written final scores for species 7 to graph file 2022-11-29 18:43:12 : Written final scores for species 0 to graph file 2022-11-29 18:43:12 : Written final scores for species 2 to graph file 2022-11-29 18:43:12 : Written final scores for species 3 to graph file 2022-11-29 18:43:12 : Written final scores for species 6 to graph file 2022-11-29 18:43:12 : Written final scores for species 9 to graph file 2022-11-29 18:43:12 : Written final scores for species 10 to graph file 2022-11-29 18:43:30 : Written final scores for species 8 to graph file 2022-11-29 18:43:32 : Written final scores for species 5 to graph file 2022-11-29 18:43:37 : Written final scores for species 4 to graph file 2022-11-29 18:43:44 : Written final scores for species 1 to graph file 2022-11-29 18:43:48 : Written final scores for species 11 to graph file
WARNING: program called by OrthoFinder produced output to stderr
Command: mcl /home/olivia/OrthoFinder_source/Proteomes_SL/primary_transcripts/OrthoFinder/Results_Nov29_1/WorkingDirectory/OrthoFinder_graph.txt -I 1.5 -o /home/olivia/OrthoFinder_source/Proteomes_SL/primary_transcripts/OrthoFinder/Results_Nov29_1/WorkingDirectory/clusters_OrthoFinder_I1.5.txt -te 16 -V all
stdout
b'' stderr
b'___ [mclvInflate] warning: nonpositive sum <0.000000> for vector 62380\n___ [mclvInflate] warning: nonpositive sum <0.000000> for vector 185839\n___ [mclvInflate] warning: nonpositive sum <0.000000> for vector 185840\n___ [mclvInflate] warning: nonpositive sum <0.000000> for vector 185842\n[mcl] added <10> garbage entries\n' 2022-11-29 18:44:46 : Ran MCL
Writing orthogroups to file
OrthoFinder assigned 228558 genes (88.8% of total) to 33368 orthogroups. Fifty percent of all genes were in orthogroups with 8 or more genes (G50 was 8) and were contained in the largest 8382 orthogroups (O50 was 8382). There were 0 orthogroups with all species present and 0 of these consisted entirely of single-copy genes.
2022-11-29 18:45:05 : Done orthogroups
Analysing Orthogroups
Calculating gene distances
2022-11-29 18:47:27 : Done Using fallback species tree inference method /home/olivia/anaconda3/envs/orthofinder_source/lib/python3.11/site-packages/numpy/core/fromnumeric.py:3432: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, /home/olivia/anaconda3/envs/orthofinder_source/lib/python3.11/site-packages/numpy/core/_methods.py:190: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount)
Inferring gene and species trees
2022-11-29 18:47:33 : Done 0 of 20790 2022-11-29 18:47:33 : Done 1000 of 20790 2022-11-29 18:47:34 : Done 2000 of 20790 2022-11-29 18:47:34 : Done 3000 of 20790 2022-11-29 18:47:34 : Done 4000 of 20790 2022-11-29 18:47:35 : Done 5000 of 20790 2022-11-29 18:47:35 : Done 6000 of 20790 2022-11-29 18:47:36 : Done 7000 of 20790 2022-11-29 18:47:36 : Done 8000 of 20790 2022-11-29 18:47:36 : Done 9000 of 20790 2022-11-29 18:47:37 : Done 10000 of 20790 2022-11-29 18:47:37 : Done 11000 of 20790 2022-11-29 18:47:37 : Done 12000 of 20790 2022-11-29 18:47:38 : Done 13000 of 20790 2022-11-29 18:47:38 : Done 14000 of 20790 2022-11-29 18:47:38 : Done 15000 of 20790 2022-11-29 18:47:38 : Done 16000 of 20790 2022-11-29 18:47:39 : Done 17000 of 20790 2022-11-29 18:47:39 : Done 18000 of 20790 2022-11-29 18:47:39 : Done 19000 of 20790 2022-11-29 18:47:40 : Done 20000 of 20790
Best outgroup(s) for species tree
2022-11-29 18:47:41 : Starting STRIDE Traceback (most recent call last): File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/stride.py", line 506, in GetRoot speciesTree = tree.Tree(speciesTreeFN, format=2) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/tree.py", line 221, in init read_newick(newick, root_node = self, format=format) File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/newick.py", line 216, in read_newick raise NewickError('Unexisting tree file or Malformed newick tree structure.') scripts_of.newick.NewickError: Unexisting tree file or Malformed newick tree structure.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/olivia/anaconda3/envs/orthofinder_source/bin/orthofinder", line 7, in
Hi
I think this might be because OrthoFinder needed an update to work with python 3.11. It was reported here and has now been resolved: https://github.com/davidemms/OrthoFinder/issues/782
Is that the same issue you were seeing?
Thanks David
Hi, I found out my error is caused because one of the inputs doesn't have a complete proteome.
Thank you.
Regards, Olivia
From: David Emms @.> Sent: Thursday, January 26, 2023 3:25 AM To: davidemms/OrthoFinder @.> Cc: #OLIVIA AGATHA# @.>; Author @.> Subject: Re: [davidemms/OrthoFinder] Version 2.5.4 NewickError Unexisting tree file but I can find tree file (Issue #768)
Hi
I think this might be because OrthoFinder needed an update to work with python 3.11. It was reported here and has now been resolved: #782https://github.com/davidemms/OrthoFinder/issues/782
Is that the same issue you were seeing?
Thanks David
— Reply to this email directly, view it on GitHubhttps://github.com/davidemms/OrthoFinder/issues/768#issuecomment-1404120477, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A4O6KPAN4EUCBVBGHFYUBYLWUF4ZZANCNFSM6AAAAAASOEWQGA. You are receiving this because you authored the thread.Message ID: @.***>