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davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
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Version 2.5.4 NewickError Unexisting tree file but I can find tree file #768

Open OliviaAgatha opened 1 year ago

OliviaAgatha commented 1 year ago

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 main(args) File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/main.py", line 1778, in main GetOrthologues(speciesInfoObj, options, prog_caller) File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/main.py", line 1540, in GetOrthologues orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/orthologues.py", line 1039, in OrthologuesWorkflow roots, clusterscounter, rootedSpeciesTreeFN, nSupport, , _, stride_dups = stride.GetRoot(spTreeFN_ids, files.FileHandler.GetOGsTreeDir(), stride.GeneToSpecies_dash, nHighParallel, qWriteRootedTree=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/stride.py", line 509, in GetRoot speciesTree = tree.Tree(speciesTreeFN, format=1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 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.

NOTE: I found tree_id.txt at .../Results_Nov29/WorkingDirectory/Tree_ids/

Please advice! Thank you!

davidemms commented 1 year ago

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

OliviaAgatha commented 1 year ago

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: @.***>

davidemms commented 1 year ago

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

davidemms commented 1 year ago

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

OliviaAgatha commented 1 year ago

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 main(args) File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/main.py", line 1778, in main GetOrthologues(speciesInfoObj, options, prog_caller) File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/main.py", line 1540, in GetOrthologues orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/orthologues.py", line 1039, in OrthologuesWorkflow roots, clusterscounter, rootedSpeciesTreeFN, nSupport, , _, stride_dups = stride.GetRoot(spTreeFN_ids, files.FileHandler.GetOGsTreeDir(), stride.GeneToSpecies_dash, nHighParallel, qWriteRootedTree=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/olivia/anaconda3/envs/orthofinder_source/bin/scripts_of/stride.py", line 509, in GetRoot speciesTree = tree.Tree(speciesTreeFN, format=1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 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.

davidemms commented 1 year ago

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

OliviaAgatha commented 1 year ago

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: @.***>