Non supported post in Github

[Belanger, Sebastien]

Hi developper,

First, thanks you for your program, this is helpful.

I posted a bud ~10 days ago on Github. But I could not get any support. Please, can you (or someone from your team) get some help?

Bellow if the bug that I reported:

################

Hi,

I followed required format to prepared my files for ete evol. See attached files. I'll report a bug when using the model b_free (the same bug is observe with the model b_neut).

Also, others models (M2, fb, fb_anc) run forever... I am surprise since I have a quite powerful machine and I run it on 10 cores. Any suggestions to make it complete the run...?

I wonder if I can get some help with the following bug:

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Command line
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dir="/Users/sbelanger/Documents/research/orthology/natural.selection"
conda activate ete3

% ete3 evol -t ${dir}/tree/DCL.aa.DCL3_4_5.nw --alg ${dir}/msa/DCL3_4_5.nt.aln.trim_NT.fasta -o ${dir}/dcl/dcl3_4_5 --models b_free --cpu 10
Using: /Users/sbelanger/opt/miniconda3/envs/ete3/bin/ete3_apps/bin/Slr
Using: /Users/sbelanger/opt/miniconda3/envs/ete3/bin/ete3_apps/bin/codeml

Running CodeML/Slr (10 CPUs)

• processing model b_free (b_free~3546a62685e886e086993d7ef74e9d7f)

Error: need branch labels in the tree for the model..
Traceback (most recent call last):
File "/Users/sbelanger/opt/miniconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete_evol.py", line 694, in load_model
File "/Users/sbelanger/opt/miniconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/evol/evoltree.py", line 436, in link_to_evol_model
File "/Users/sbelanger/opt/miniconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/evol/model.py", line 171, in _load
KeyError: 'lnL'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/sbelanger/opt/miniconda3/envs/ete3/bin/ete3", line 33, in 
sys.exit(load_entry_point('ete3==3.1.2', 'console_scripts', 'ete3')())
File "/Users/sbelanger/opt/miniconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete.py", line 95, in main
File "/Users/sbelanger/opt/miniconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete.py", line 269, in _main
File "/Users/sbelanger/opt/miniconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete_evol.py", line 905, in run
File "/Users/sbelanger/opt/miniconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete_evol.py", line 697, in load_model
Exception: ERROR: model b_free failed, problem with outfile:
/Users/sbelanger/Documents/research/orthology/natural.selection/dcl/dcl3_4_5/b_free~3546a62685e886e086993d7ef74e9d7f/out

######################

Thanks!!
Sébastien

Best regard,
Sébastien

——————————————————
Sébastien Bélanger, Ph. D
Research Scientist
Meyers Lab
Donald Danforth Plant Science Center
975 N Warson Rd
St. Louis, MO 63132
USA

Best regard,
Sébastien

——————————————————
Sébastien Bélanger, Ph. D
Research Scientist
Meyers Lab
Donald Danforth Plant Science Center
975 N Warson Rd
St. Louis, MO 63132
USA

[ziqi deng]

Hi,

it seems you were trying to use model of b_free, which is branch model, and ach branch model will be run on each set of marks. Hence I found the chapter of Marking trees from  http://etetoolkit.org/documentation/ete-evol/ which very similar to your case. If it still doesn't work, it would be helpful if you provide the related dataset.

Cheers,

Ziqi

Belanger, Sebastien <SBel...@danforthcenter.org> 于2021年5月29日周六 下午5:19写道：

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[dengzi...@gmail.com]

And in regards to the running time, we realized it already and we are currently working on it by putting it onto the cloud service so your don't have to spend your PC/server resources for evol analysis. Stay tuned :)

Cheers,

Ziqi 

[Sébastien Bélanger]

Hi Ziqi,

I don’t know why, but I cannot port on the google group that you gave me.

So I will do it here.

#######

Thanks for the reply. I know the chapter. I read it. The same message error arise with or without the --mark option and with different branch model (). 

I attached my file to this post. Below, I list some command line used:

dir="/Users/sbelanger/Documents/research/orthology/natural.selection"

conda activate ete3

ete3 evol -t ${dir}/tree/DCL.aa.DCL3_4_5.nw --alg ${dir}/msa/DCL3_4_5.nt.aln.trim_NT.fasta  -o ${dir}/dcl/dcl3_4_5  --models b_free --cpu 10

ete3 evol -t ${dir}/tree/DCL.aa.DCL3_4_5.nw --alg ${dir}/msa/DCL3_4_5.nt.aln.trim_NT.fasta  -o ${dir}/dcl/dcl3_4_5  --models b_neut --cpu 10

ete3 evol -t ${dir}/tree/DCL.aa.DCL3_4_5.nw --alg ${dir}/msa/DCL3_4_5.nt.aln.trim_NT.fasta  -o ${dir}/dcl/dcl3_4_5  --models fb_anc --cpu 10

These two takes forever to run... I stop to run it since previous command lines bugs to report results.

ete3 evol -t ${dir}/tree/DCL.aa.DCL3_4_5.nw --alg ${dir}/msa/DCL3_4_5.nt.aln.trim_NT.fasta  -o ${dir}/dcl/dcl3_4_5  --models M2 --cpu 10

ete3 evol -t ${dir}/tree/DCL.aa.DCL3_4_5.nw --alg ${dir}/msa/DCL3_4_5.nt.aln.trim_NT.fasta  -o ${dir}/dcl/dcl3_4_5  --models fb --cpu 10

See attached files.

Thanks 

Sébastien

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