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.
I have successfully run branch models in ete3 and wanted to run site models and branch-site models on the same dataset. Unfortunately both of these are causing me errors:
SUMMARY BY MODEL
Model M8a
Average omega for all tree: 1.000
Traceback (most recent call last):
File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete_evol.py", line 950, in run
File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/evol/model.py", line 335, in significance_by_site
KeyError: 'BEB'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete_evol.py", line 953, in run
File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/evol/model.py", line 335, in significance_by_site
KeyError: 'NEB'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/kathy/opt/anaconda3/envs/ete3/bin/ete3", line 33, in
sys.exit(load_entry_point('ete3==3.1.2', 'console_scripts', 'ete3')())
File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete.py", line 95, in main
File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete.py", line 269, in _main
File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete_evol.py", line 955, in run
File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/evol/model.py", line 335, in significance_by_site
KeyError: 'SLR'
Build check seems fine:
Current Toolchain path: /Users/kathy/opt/anaconda3/envs/ete3/bin/ete3_apps/bin
Current Toolchain version: unknown
clustalo: MISSING
codeml: OK - AAML in paml version 4.8a, July 2014
Dialign-tx not supported in OS X
fasttree: OK - Usage for FastTree version 2.1.8 Double precision (No SSE3), OpenMP (1 threads):
iqtree: OK - IQ-TREE multicore version 1.5.5 for Mac OS X 64-bit built Jun 2 2017
kalign: OK - Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann
mafft: OK - MAFFT v6.861b (2011/09/24)
muscle: OK - MUSCLE v3.8.31 by Robert C. Edgar
phyml: OK - . This is PhyML version 20160115.
pmodeltest: OK - pmodeltest.py v1.4
raxml: OK - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
raxml-pthreads: OK - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
readal: OK - readAl v1.4.rev6 build[2012-02-02]
slr: OK - # SLR "Sitewise Likelihood Ratio" selection detection program. Version 1.4.3
statal: OK - statAl v1.4.rev6 build[2012-02-02]
tcoffee: OK - PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477)
trimal: OK - trimAl v1.4.rev6 build[2012-02-02]
Hello,
I have successfully run branch models in ete3 and wanted to run site models and branch-site models on the same dataset. Unfortunately both of these are causing me errors:
SUMMARY BY MODEL
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete_evol.py", line 953, in run File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/evol/model.py", line 335, in significance_by_site KeyError: 'NEB'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/Users/kathy/opt/anaconda3/envs/ete3/bin/ete3", line 33, in
sys.exit(load_entry_point('ete3==3.1.2', 'console_scripts', 'ete3')())
File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete.py", line 95, in main
File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete.py", line 269, in _main
File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools/ete_evol.py", line 955, in run
File "/Users/kathy/opt/anaconda3/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/evol/model.py", line 335, in significance_by_site
KeyError: 'SLR'
Build check seems fine: Current Toolchain path: /Users/kathy/opt/anaconda3/envs/ete3/bin/ete3_apps/bin Current Toolchain version: unknown clustalo: MISSING codeml: OK - AAML in paml version 4.8a, July 2014 Dialign-tx not supported in OS X fasttree: OK - Usage for FastTree version 2.1.8 Double precision (No SSE3), OpenMP (1 threads): iqtree: OK - IQ-TREE multicore version 1.5.5 for Mac OS X 64-bit built Jun 2 2017 kalign: OK - Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann mafft: OK - MAFFT v6.861b (2011/09/24) muscle: OK - MUSCLE v3.8.31 by Robert C. Edgar phyml: OK - . This is PhyML version 20160115. pmodeltest: OK - pmodeltest.py v1.4 raxml: OK - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017. raxml-pthreads: OK - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017. readal: OK - readAl v1.4.rev6 build[2012-02-02] slr: OK - # SLR "Sitewise Likelihood Ratio" selection detection program. Version 1.4.3 statal: OK - statAl v1.4.rev6 build[2012-02-02] tcoffee: OK - PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477) trimal: OK - trimAl v1.4.rev6 build[2012-02-02]
Any thoughts on what might be causing this?
Thanks, Kathy