Question: ete3 evol doesnt work on test data
0
gravatar for Kay
11 months ago by
Kay0
Liverpool, UK
Kay0 wrote:

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 • 541 views
ADD COMMENTlink modified 11 months ago by WouterDeCoster41k • written 11 months ago by Kay0

Check if your ETE3 toolkit is the latest version:

TypeError: Unicode-objects must be encoded before hashing

Problem getting ete3 evol up and running

ADD REPLYlink written 11 months ago by h.mon27k

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)

ADD REPLYlink written 11 months ago by Kay0
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