Error: during Running Orthologue Prediction

[qiao-xin]

Running Orthologue Prediction

1. Checking required programs are installed

Test can run "fastme -i myfilepath/SimpleTest.phy -o myfilepath/SimpleTest.tre" - ok
Test can run "dlcpar_search --version" - ok

2. Calculating gene distances

2016-09-15 09:39:04 : Done 20 of 49
2016-09-15 09:38:40 : Done 0 of 49
2016-09-15 09:38:53 : Done 10 of 49
2016-09-15 09:39:15 : Done 30 of 49
2016-09-15 09:39:29 : Processing species 0
2016-09-15 09:40:08 : Processing species 1
2016-09-15 09:40:43 : Processing species 2
2016-09-15 09:41:24 : Processing species 3
2016-09-15 09:43:03 : Processing species 4
2016-09-15 09:43:33 : Processing species 5
2016-09-15 09:44:03 : Processing species 6

3. Inferring gene and species trees

. Error: Invalid distance matrix : numerical value expected for taxon '5_6492' instead of '-inf'.
2016-09-15 09:45:33 : Done 4000 of 10413
2016-09-15 09:45:13 : Done 1000 of 10413

4. Best outgroup(s) for species tree

Traceback (most recent call last):
File "orthofinder.py", line 1190, in
orthologuesResultsFilesString = get_orthologues.GetOrthologues(workingDir, resultsDir, clustersFilename_pairs, nBlast)
File "/home/george/programs/OrthoFinder-master/orthofinder/scripts/get_orthologues.py", line 566, in GetOrthologues
roots, clusters, rootedSpeciesTreeFN, nSupport = rfd.GetRoot(spTreeFN_ids, os.path.split(db.treesPatIDs)[0] + "/", rfd.GeneToSpecies_dash, nProcesses, treeFmt = 1)
File "/home/george/programs/OrthoFinder-master/orthofinder/scripts/root_from_duplications.py", line 401, in GetRoot
list_of_lists = pool.map(SupportedHierachies_wrapper2, [(fn, GeneToSpeciesMap, species, dict_clades, clade_names) for fn in glob.glob(treesDir + "/*")])
File "/home/george/anaconda2/lib/python2.7/multiprocessing/pool.py", line 251, in map
return self.map_async(func, iterable, chunksize).get()
File "/home/george/anaconda2/lib/python2.7/multiprocessing/pool.py", line 567, in get
raise self._value
scripts.newick.NewickError: Unexisting tree file or Malformed newick tree structure.
2016-09-15 09:35:32 : Writen final scores for species 0 to graph file
2016-09-15 09:35:43 : Writen final scores for species 1 to graph file
2016-09-15 09:35:54 : Writen final scores for species 2 to graph file
2016-09-15 09:36:17 : Writen final scores for species 3 to graph file
2016-09-15 09:36:27 : Writen final scores for species 4 to graph file
2016-09-15 09:36:36 : Writen final scores for species 5 to graph file
2016-09-15 09:36:45 : Writen final scores for species 6 to graph file

How to handle this error?

[mjfi2sb3]

Hi,
has anyone addressed this error? I am looking at the same error and I cannot tell the seriousness of it

Regards,
/SB

[davidemms]

Hi, could you find the "WorkingDirectory" that has the Blast*.txt files in it and run "grep 5_6492 Blast*txt" in that directory and paste the output that you get?

Many thanks
David

[davidemms]

... and could you also let me know what version of OrthoFinder you are using please? Thanks

[qiao-xin]

@davidemms Many thanks for your kind reply. According to your suggestion, the command was ran, and the results are as follows:
Blast3_5.txt:3_49031 5_6492 65.00 60 21 0 3 62 3 62 3e-12 58.2
Blast5_3.txt:5_6492 3_49031 65.00 60 21 0 3 62 3 62 3e-12 58.2
Blast5_5.txt:5_6492 5_6492 100.00 87 0 0 1 87 1 87 2e-41 133

In addition, I can find the directory "Orthologues" in the "WorkingDirectory", however, the "Orthologues" only contained dir "Gene_Trees" and "WorkingDirectory", and this is incomplete.

I downloaded the OrthoFinder on Sep. 14, 2016. This version should be the latest version.

Thanks

[qiao-xin]

@davidemms If you need to check any related data files, I am very pleased to upload it.

[davidemms]

I can't see at the moment want the cause of the error might be. Would you mind sharing the dataset with me if it is not too large? I would need a tar.gz or zip file of the WorkingDirectory (the one where you ran the grep command). Dropbox would be the best way to send the data to me. If this is ok then send me an email and I will send you an invite to a dropbox folder that you can put the compressed dataset in.

Thanks
David

[davidemms]

The problem was caused by a rare case where in the BLAST searches a sequence was hit by one sequence but when it was used as the query it didn't hit anything.

[mjfi2sb3]

so is this problem solved?

do I need to re-run orthofinder or I can just restart from the blast results?

[qiao-xin]

@mjfi2sb3 Yes, this problem has been solved by Davide. You need to download the latest version of the OrthoFinder from GitHub and re-run it.

[davidemms]

You can restart from the BLAST results.

All the best
David

[CIWa]

Hello everyone,

During the last week I ran into a similar problem while running version 1.1.4. and while using MSA. My error message was

Best outgroup(s) for species tree

Traceback (most recent call last):
File "orthofinder/orthofinder.py", line 1354, in
File "orthofinder/orthofinder.py", line 1242, in GetOrthologues
File "orthofinder/scripts/get_orthologues.py", line 746, in OrthologuesWorkflow
File "orthofinder/scripts/root_from_duplications.py", line 405, in GetRoot
File "multiprocessing/pool.py", line 250, in map
File "multiprocessing/pool.py", line 554, in get
scripts.newick.NewickError: Unexisting tree file or Malformed newick tree structure.
Failed to execute script orthofinder
2017-06-30 20:44:28 : Writen final scores for species 3 to graph file
2017-06-30 20:44:28 : Writen final scores for species 4 to graph file
2017-06-30 20:44:30 : Writen final scores for species 9 to graph file
2017-06-30 20:44:30 : Writen final scores for species 5 to graph file
2017-06-30 20:44:44 : Writen final scores for species 0 to graph file
2017-06-30 20:44:47 : Writen final scores for species 8 to graph file
2017-06-30 20:44:50 : Writen final scores for species 10 to graph file
2017-06-30 20:44:58 : Writen final scores for species 2 to graph file
2017-06-30 20:46:23 : Writen final scores for species 6 to graph file

I will try again using version 1.1.8.

Best, Isabel

[CIWa]

Hi everyone,

With exactly the same data version 1.1.8 seems to have no problem.

Best,
Isabel

[drkmj]

Hi all,

I have run across this error too. I am using OrthoFinder version 2.1.0.

Any ideas what I can do to resolve this error?

Analysing Orthogroups

Calculating gene distances

2017-10-28 09:24:43 : Done 0 of 25
2017-10-28 09:42:27 : Done 10 of 25
2017-10-28 09:48:35 : Done 20 of 25
2017-10-28 09:50:58 : Processing species 0
2017-10-28 09:53:59 : Processing species 1
2017-10-28 09:54:21 : Processing species 2
2017-10-28 09:54:33 : Processing species 3
2017-10-28 09:54:52 : Processing species 4

Inferring gene and species trees

2017-10-28 09:55:40 : Done 0 of 9161
2017-10-28 09:59:33 : Done 1000 of 9161
2017-10-28 09:59:43 : Done 2000 of 9161
2017-10-28 09:59:52 : Done 3000 of 9161
2017-10-28 10:00:01 : Done 4000 of 9161
2017-10-28 10:00:11 : Done 5000 of 9161
2017-10-28 10:00:20 : Done 6000 of 9161
2017-10-28 10:00:29 : Done 7000 of 9161
2017-10-28 10:00:39 : Done 8000 of 9161
2017-10-28 10:00:48 : Done 9000 of 9161

Best outgroup(s) for species tree

Traceback (most recent call last):
File "orthofinder.py", line 1533, in
GetOrthologues(dirs, options, program_caller, clustersFilename_pairs, orthogroupsResultsFilesString)
File "orthofinder.py", line 1365, in GetOrthologues
options.separatePickleDir)
File "/Users/kjohnson/OrthoFinder-master/orthofinder/scripts/orthologues.py", line 924, in OrthologuesWorkflow
roots, clusters_counter, rootedSpeciesTreeFN, nSupport, _, _, all_stride_dup_genes = stride.GetRoot(spTreeFN_ids, os.path.split(db.TreeFilename_IDs(0))[0] + "/", stride.GeneToSpecies_dash, nHighParallel, treeFmt = 1, qWriteRootedTree=True)
File "/Users/kjohnson/OrthoFinder-master/orthofinder/scripts/stride.py", line 499, in GetRoot
list_of_dicts = pool.map(SupportedHierachies_wrapper2, [(fn, GeneToSpeciesMap, species, dict_clades, clade_names, qWriteDupTrees) for fn in glob.glob(treesDir + "/*")])
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/pool.py", line 251, in map
return self.map_async(func, iterable, chunksize).get()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/pool.py", line 567, in get
raise self._value
scripts.newick.NewickError: Unexisting tree file or Malformed newick tree structure.

Thank you,
Kevin