ete3 evol doesnt work on test data
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2.4 years ago
Kay ▴ 10

Hi, I recently installed ete via conda, so have a new environment for ete. I was able to use it to generate trees using

ete3 build -w standard_raxml -a NUP62.aa.fa -o output_tree

but when I try to run:

ete3 evol -t ECP_EDN_15.nw --alg ECP_EDN_15.fasta -o results1/ --models fb M2 SLR --cpu 3

using the test data, it doesn't work.

Error says:

Running CodeML/Slr (3 CPUs)
Traceback (most recent call last):
  File "/pub38/kayussky/anaconda3/envs/ete/bin/ete3", line 11, in <module>
    load_entry_point('ete3==3.1.1', 'console_scripts', 'ete3')()
  File "/pub38/kayussky/anaconda3/envs/ete/lib/python3.6/site-packages/ete3/tools/ete.py", line 95, in main
    _main(sys.argv)
  File "/pub38/kayussky/anaconda3/envs/ete/lib/python3.6/site-packages/ete3/tools/ete.py", line 268, in _main
    args.func(args)
  File "/pub38/kayussky/anaconda3/envs/ete/lib/python3.6/site-packages/ete3/tools/ete_evol.py", line 900, in run
    models.update(run_all_models(tree, nodes, marks, args, **params))
  File "/pub38/kayussky/anaconda3/envs/ete/lib/python3.6/site-packages/ete3/tools/ete_evol.py", line 528, in run_all_models
    print('  - processing model %s (%s)' % (model, name_model(tree, model)))
  File "/pub38/kayussky/anaconda3/envs/ete/lib/python3.6/site-packages/ete3/tools/ete_evol.py", line 457, in name_model
    base_name).hexdigest()
TypeError: Unicode-objects must be encoded before hashing

trying with ete instead of ete3 says:

Traceback (most recent call last):
  File "/usr/local/bin/ete", line 5, in <module>
    from pkg_resources import load_entry_point
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2957, in <module>

  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 567, in _build_master

  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 876, in require

  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 761, in resolve

pkg_resources.DistributionNotFound: ete2==2.3.10

Not particularly sure what to do. Kay

ete paml ete3 • 1.4k views
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thanks, seems to work on the test data, and paml test data now, I installed ete toolkit from github in a new conda environment

although my data returns a few errors (might gahe to do with my data)

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