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etetoolkit / ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
http://etetoolkit.org
GNU General Public License v3.0
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Bug: ERROR: model b_free failed, problem with outfile: #526

Open sebel76 opened 3 years ago

sebel76 commented 3 years ago

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:

########## Command line ########## 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)

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

sebel76 commented 3 years ago

Please, can I get support for this bug? I posted it ~10 days ago. Thanks.

dengzq1234 commented 3 years ago

sorry for the delay, hope it helps. https://groups.google.com/g/etetoolkit/c/_I84g4uCqJE

sebel76 commented 3 years ago

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