Error: need branch labels in the tree for the model..

[Gaius Marius]

Hi ETE3 team, 

Thanks for such a great tool. Out of the ~20,000 genes I am analysing, for ~500 I am getting the below error message: 

Error: need branch labels in the tree for the model..
Error: need branch labels in the tree for the model..
Traceback (most recent call last):
File "/rds/general/user/cm1118/home/anaconda3/envs/ete3_env/lib/python3.6/site-packages/ete3-3.1.1-py3.6.egg/ete3/tools/ete_evol.py", line 694, in load_model
tree.link_to_evol_model(path, model_obj)
File "/rds/general/user/cm1118/home/anaconda3/envs/ete3_env/lib/python3.6/site-packages/ete3-3.1.1-py3.6.egg/ete3/evol/evoltree.py", line 436, in link_to_evol_model
model._load(path)
File "/rds/general/user/cm1118/home/anaconda3/envs/ete3_env/lib/python3.6/site-packages/ete3-3.1.1-py3.6.egg/ete3/evol/model.py", line 171, in _load
vars(self) ['lnL'] = self.stats ['lnL']
KeyError: 'lnL'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/rds/general/user/cm1118/home/anaconda3/envs/ete3_env/bin/ete3", line 11, in 
load_entry_point('ete3==3.1.1', 'console_scripts', 'ete3')()
File "/rds/general/user/cm1118/home/anaconda3/envs/ete3_env/lib/python3.6/site-packages/ete3-3.1.1-py3.6.egg/ete3/tools/ete.py", line 95, in main
_main(sys.argv)
File "/rds/general/user/cm1118/home/anaconda3/envs/ete3_env/lib/python3.6/site-packages/ete3-3.1.1-py3.6.egg/ete3/tools/ete.py", line 268, in _main
args.func(args)
File "/rds/general/user/cm1118/home/anaconda3/envs/ete3_env/lib/python3.6/site-packages/ete3-3.1.1-py3.6.egg/ete3/tools/ete_evol.py", line 905, in run
load_model(model, tree, models[model], **params)
File "/rds/general/user/cm1118/home/anaconda3/envs/ete3_env/lib/python3.6/site-packages/ete3-3.1.1-py3.6.egg/ete3/tools/ete_evol.py", line 697, in load_model
model_obj.name, path)))
Exception: ERROR: model b_neut.26-1 failed, problem with outfile:
/rds/general/user/cm1118/projects/neurogenomics-lab/ephemeral/EvolutionOfCelltypes/multiz_hg38_30-way_LotsMoreModels_June2020/ucscGenes/DEFA5/DEFA5-evol-branch/b_neut.26-1~3439f64eaf71d490dbbced5a104d3a3e/out

I think it has something to do with the number of parentheses in the newick tree file but I'm not sure how to resolve this. 

I have also attached an example fasta file and newick file for which I am getting this error. 

Thank you!

[dengzi...@gmail.com]

Hi, could you provide the command you run upon this error? Thanks

[Gaius Marius]

Thanks for getting back to me. Bit of a slow reply on my part but here it is:

ete3 evol -t species_tree.nw --alg DEFA5-clean.fasta -o DEFA5-branch --models M0 b_neut b_free --tests b_free,M0 b_free,b_neut --cpu 16 --mark hg38 hg38,,panTro5  hg38,,otoGar3 >> DEFA5.branch.log

[fransua]

Hi,

sorry for the late reply.

I think the problem is marking the root of the tree,  you need an outgroup for codeml to have something to compare with.

let me know if this helps

pd: great thanks for using the tool like this with complex marking scheme... I was told nobody would ever understand/use this :)

(see Jaime!!! :P )

cheers

francois

[GenomeBrowser]

This makes sense, I can now see that for these fasta files we are missing sequences for the out group species. Thank you for your help!