ete3 build fails
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sunny kevin
Jul 17, 2022, 7:25:46 AM7/17/22
to The ETE toolkit
Hello everyone,
Can some one help me in building the ete3. I installed it manually,
ete3 upgrade-external-tools. I exported this path as well in my .bashrc
Need help, how do I solve the below error.
ete 3 build only works with python 3.4 ?
cmd -
ete3 build -n OG0022535.all.r.fa -o tree4 --logfile -C 8 -w eggnog41 --clearall
Toolchain path: /home/sun/anaconda3/bin/ete3_apps/bin Toolchain version: unknown
WARNING: external applications directory are not found at /home/sun/anaconda3/bin/ete3_apps/bin
Use "ete build install_tools" to install or upgrade tools
['metaligner_trimmed-trimal01-prottest_default-phyml_default']
--------------------------------------------------------------------------------
ETE build (3.1.2) - reproducible phylogenetic workflows
Citation:
Huerta-Cepas J, Serra F and Bork P. ETE 3: Reconstruction, analysis and
visualization of phylogenomic data. Mol Biol Evol (2016)
doi:10.1093/molbev/msw046
(Note that a list of the external programs used to complete all necessary
computations will be shown after workflow execution. Those programs should
also be cited.)
--------------------------------------------------------------------------------
INFO - Testing x86-64 portable applications...
clustalo: MISSING
dialigntx: MISSING
fasttree: MISSING
iqtree: MISSING
kalign: MISSING
mafft: MISSING
muscle: MISSING
phyml: MISSING
pmodeltest: MISSING
raxml: MISSING
raxml-pthreads: MISSING
readal: MISSING
statal: MISSING
tcoffee: MISSING
trimal: MISSING
WARNING: 15 external tools seem to be missing or unfunctional
Install using conda (recomended):
conda install -c etetoolkit ete3_external_apps
or manually compile by running:
ete3 upgrade-external-tools
INFO - Starting ETE-build execution at Sun Jul 17 11:21:37 2022
INFO - Output directory /DATA/ecology/sun/softwares/evaluation/paml-master/src/result5/lumpsuckers/newtestrun/hypto/OG0019520/pamlfiles/modell0/1880cdsfiles/ete3/spectree/tree4
INFO - Erasing all existing npr data...
WRNG - Using existing dir: /DATA/ecology/sun/softwares/evaluation/paml-master/src/result5/lumpsuckers/newtestrun/hypto/OG0019520/pamlfiles/modell0/1880cdsfiles/ete3/spectree/tree4/db
INFO - Reading nt sequences from OG0022535.all.r.fa...
WRNG - 10 target sequences
INFO - ETE build starts now!
Traceback (most recent call last):
File "/home/sun/anaconda3/bin/ete3", line 33, in <module>
sys.exit(load_entry_point('ete3==3.1.2', 'console_scripts', 'ete3')())
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete.py", line 95, in main
_main(sys.argv)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete.py", line 147, in _main
ete_build._main(arguments, builtin_apps_path)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build.py", line 1102, in _main
app_wrapper(main, args)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/interface.py", line 372, in app_wrapper
main(None, func, args)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/interface.py", line 494, in main
func(args)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build.py", line 615, in main
new_tasks = pipeline(None, wkname, config)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/workflow/genetree.py", line 472, in pipeline
db.add_node(initial_task.threadid, initial_task.nodeid,
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/db.py", line 381, in add_node
[nodeid, cladeid, encode(targets),
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/db.py", line 72, in encode
return bytes.decode(base64.encodestring(six.moves.cPickle.dumps(x, 2)))
AttributeError: module 'base64' has no attribute 'encodestring'
dengzi...@gmail.com
Jul 17, 2022, 8:25:34 AM7/17/22
to The ETE toolkit
Hi,
the program shows you lack of some external tool for executing the workflow
I can be done by running
`conda install -c etetoolkit ete_toolchain`
for further detail please find http://etetoolkit.org/download/
best
Ziqi
sunny kevin
Jul 17, 2022, 10:05:36 AM7/17/22
to The ETE toolkit
Hello again,
Do i have to change the python version ? Suggestions please!
conda install -c etetoolkit ete_toolchain
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- ete_toolchain -> python[version='>=2.7,<2.8.0a0|>=3.4,<3.5.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']
Your python: python=3.9
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.31=0
- feature:|@/linux-64::__glibc==2.31=0
Your installed version is: 2.31
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- ete_toolchain -> python[version='>=2.7,<2.8.0a0|>=3.4,<3.5.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']
Your python: python=3.9
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.31=0
- feature:|@/linux-64::__glibc==2.31=0
Your installed version is: 2.31
ziqi deng
Jul 17, 2022, 10:11:25 AM7/17/22
to eteto...@googlegroups.com
I see, the reason is one of the tools in ete_toolchain, pmodeltest, is not available when py > 3.6. Your work doesn't need this tool as I see. So you can
1) change to py3.6 and run the conda install -c etetoolkit ete_toolchain
2) keep on py3.9, but install alignment and tree building tools from https://anaconda.org/etetoolkit/repo one by one
Ziqi
sunny kevin <sunnyk...@gmail.com> 于2022年7月17日周日 16:05写道：
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sunny kevin
Jul 18, 2022, 5:44:45 AM7/18/22
to The ETE toolkit
I try to install etetoolkit. Only python 2.7 or python 3.6 supports ?
I had python 3.9V.
Suggestions please!
conda install -c etetoolkit ete_toolchain
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- ete_toolchain -> python[version='>=2.7,<2.8.0a0|>=3.4,<3.5.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']
Your python: python=3.9
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.31=0
- feature:|@/linux-64::__glibc==2.31=0
Your installed version is: 2.31
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- ete_toolchain -> python[version='>=2.7,<2.8.0a0|>=3.4,<3.5.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']
Your python: python=3.9
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.31=0
- feature:|@/linux-64::__glibc==2.31=0
Your installed version is: 2.31
On Sunday, July 17, 2022 at 2:25:34 PM UTC+2 dengzi...@gmail.com wrote:
sunny kevin
Jul 18, 2022, 5:44:45 AM7/18/22
to The ETE toolkit
Hello Ziqi,
After installing all the dependencies, ending up with a similar error.
AttributeError: module 'base64' has no attribute 'encodestring'
I installed the base64 package.
Toolchain path: /home/sun/anaconda3/bin/ete3_apps/bin
Toolchain version: unknown
Toolchain version: unknown
['metaligner_trimmed-trimal01-prottest_default-phyml_default']
--------------------------------------------------------------------------------
ETE build (3.1.2) - reproducible phylogenetic workflows
Citation:
Huerta-Cepas J, Serra F and Bork P. ETE 3: Reconstruction, analysis and
visualization of phylogenomic data. Mol Biol Evol (2016)
doi:10.1093/molbev/msw046
(Note that a list of the external programs used to complete all necessary
computations will be shown after workflow execution. Those programs should
also be cited.)
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
ETE build (3.1.2) - reproducible phylogenetic workflows
Citation:
Huerta-Cepas J, Serra F and Bork P. ETE 3: Reconstruction, analysis and
visualization of phylogenomic data. Mol Biol Evol (2016)
doi:10.1093/molbev/msw046
(Note that a list of the external programs used to complete all necessary
computations will be shown after workflow execution. Those programs should
also be cited.)
--------------------------------------------------------------------------------
^[[32mINFO^[[0m - Testing x86-64 portable applications...
clustalo: ^[[32mOK^[[0m - 1.2.4
dialigntx: ^[[32mOK^[[0m - This is DIALIGN-TX Version 1.0.2 - A Multiple Sequence alignment program.
fasttree: ^[[32mOK^[[0m - Usage for FastTree version 2.1.8 Double precision (No SSE3), OpenMP (2 threads):
iqtree: ^[[32mOK^[[0m - IQ-TREE multicore version 1.5.5 for Linux 64-bit built Jun 2 2017
kalign: ^[[32mOK^[[0m - Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann
mafft: ^[[32mOK^[[0m - MAFFT v6.861b (2011/09/24)
muscle: ^[[32mOK^[[0m - MUSCLE v3.8.31 by Robert C. Edgar
phyml: ^[[32mOK^[[0m - . This is PhyML version 20160115.
pmodeltest: ^[[31mMISSING^[[0m
raxml: ^[[32mOK^[[0m - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
raxml-pthreads: ^[[32mOK^[[0m - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
readal: ^[[32mOK^[[0m - readAl v1.4.rev6 build[2012-02-02]
statal: ^[[32mOK^[[0m - statAl v1.4.rev6 build[2012-02-02]
tcoffee: ^[[31mMISSING^[[0m
trimal: ^[[32mOK^[[0m - trimAl v1.4.rev6 build[2012-02-02]
^[[1;33m
WARNING: 2 external tools seem to be missing or unfunctional^[[0m
^[[1;32mInstall using conda (recomended):^[[0m
^[[0m conda install -c etetoolkit ete3_external_apps^[[0m
^[[1;32mor manually compile by running:^[[0m
^[[0m ete3 upgrade-external-tools^[[0m
^[[32mINFO^[[0m - Starting ETE-build execution at Sun Jul 17 21:34:29 2022
^[[32mINFO^[[0m - Output directory /home/sun/data/softwares/ete-3.1.2/ete3/tree4.1
^[[32mINFO^[[0m - Erasing all existing npr data...
^[[32mINFO^[[0m - Reading nt sequences from OG0022535.all.r.fa...
^[[1;37;43mWRNG^[[0m - 10 target sequences
^[[32mINFO^[[0m - ETE build starts now!
clustalo: ^[[32mOK^[[0m - 1.2.4
dialigntx: ^[[32mOK^[[0m - This is DIALIGN-TX Version 1.0.2 - A Multiple Sequence alignment program.
fasttree: ^[[32mOK^[[0m - Usage for FastTree version 2.1.8 Double precision (No SSE3), OpenMP (2 threads):
iqtree: ^[[32mOK^[[0m - IQ-TREE multicore version 1.5.5 for Linux 64-bit built Jun 2 2017
kalign: ^[[32mOK^[[0m - Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann
mafft: ^[[32mOK^[[0m - MAFFT v6.861b (2011/09/24)
muscle: ^[[32mOK^[[0m - MUSCLE v3.8.31 by Robert C. Edgar
phyml: ^[[32mOK^[[0m - . This is PhyML version 20160115.
pmodeltest: ^[[31mMISSING^[[0m
raxml: ^[[32mOK^[[0m - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
raxml-pthreads: ^[[32mOK^[[0m - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
readal: ^[[32mOK^[[0m - readAl v1.4.rev6 build[2012-02-02]
statal: ^[[32mOK^[[0m - statAl v1.4.rev6 build[2012-02-02]
tcoffee: ^[[31mMISSING^[[0m
trimal: ^[[32mOK^[[0m - trimAl v1.4.rev6 build[2012-02-02]
^[[1;33m
WARNING: 2 external tools seem to be missing or unfunctional^[[0m
^[[1;32mInstall using conda (recomended):^[[0m
^[[0m conda install -c etetoolkit ete3_external_apps^[[0m
^[[1;32mor manually compile by running:^[[0m
^[[0m ete3 upgrade-external-tools^[[0m
^[[32mINFO^[[0m - Starting ETE-build execution at Sun Jul 17 21:34:29 2022
^[[32mINFO^[[0m - Output directory /home/sun/data/softwares/ete-3.1.2/ete3/tree4.1
^[[32mINFO^[[0m - Erasing all existing npr data...
^[[32mINFO^[[0m - Reading nt sequences from OG0022535.all.r.fa...
^[[1;37;43mWRNG^[[0m - 10 target sequences
^[[32mINFO^[[0m - ETE build starts now!
Traceback (most recent call last):
File "/home/sun/anaconda3/bin/ete3", line 33, in <module>
sys.exit(load_entry_point('ete3==3.1.2', 'console_scripts', 'ete3')())
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete.py", line 95, in main
_main(sys.argv)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete.py", line 147, in _main
ete_build._main(arguments, builtin_apps_path)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build.py", line 1102, in _main
app_wrapper(main, args)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/interface.py", line 372, in app_wrapper
main(None, func, args)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/interface.py", line 494, in main
func(args)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build.py", line 615, in main
new_tasks = pipeline(None, wkname, config)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/workflow/genetree.py", line 472, in pipeline
db.add_node(initial_task.threadid, initial_task.nodeid,
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/db.py", line 381, in add_node
[nodeid, cladeid, encode(targets),
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/db.py", line 72, in encode
return bytes.decode(base64.encodestring(six.moves.cPickle.dumps(x, 2)))
AttributeError: module 'base64' has no attribute 'encodestring'
72,3 Bot
sunny kevin
Jul 18, 2022, 5:44:45 AM7/18/22
to The ETE toolkit
I made the python3.6 environment, and installed the "conda install -c etetoolkit ete_toolchain"
When I execute the below command -
ete3 build -n OG0022535.all.r.fa -o tree4 --logfile -C 8 -w eggnog41 --clearall
What does the -w ? how do I select the workflow ? I couldn't find it in the manual.
After installing all the dependencies, still their was some tools are missing.
I don't really understand why it is showing on the prompt.
INFO - Testing x86-64 portable applications...
clustalo: OK - 1.2.4
dialigntx: MISSING
fasttree: OK - Usage for FastTree version 2.1.8 Double precision (No SSE3), OpenMP (2 threads):
dialigntx: MISSING
fasttree: OK - Usage for FastTree version 2.1.8 Double precision (No SSE3), OpenMP (2 threads):
iqtree: MISSING
kalign: MISSING
mafft: MISSING
muscle: MISSING
phyml: OK - . This is PhyML version 20160115.
pmodeltest: MISSING
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]
statal: OK - statAl v1.4.rev6 build[2012-02-02]
pmodeltest: MISSING
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]
statal: OK - statAl v1.4.rev6 build[2012-02-02]
Suggestions appreciated.
On Sunday, July 17, 2022 at 4:11:25 PM UTC+2 dengzi...@gmail.com wrote:
ziqi deng
Jul 18, 2022, 5:54:12 AM7/18/22
to eteto...@googlegroups.com
Hi,
workflows information can be checked in this tutorial
here is further detail(this file will be generated when you execute ete3 build)
at your case
eggnog41=metaligner_trimmed-trimal01-prottest_default-phyml_default
If there are still apps missing, the etetoolkit repo is available to install app individually https://anaconda.org/etetoolkit/repo
Ziqi
sunny kevin <sunnyk...@gmail.com> 于2022年7月18日周一 11:44写道：
To view this discussion on the web visit https://groups.google.com/d/msgid/etetoolkit/c5c3aa76-6e50-46cb-b67b-81f92d1df436n%40googlegroups.com.
sunny kevin
Jul 18, 2022, 8:54:17 AM7/18/22
to The ETE toolkit
Hello again, I reinstalled the packages, ending up with error. How do I solve this below error ??
AttributeError: module 'base64' has no attribute 'encodestring'
Toolchain path: /home/sun/anaconda3/bin/ete3_apps/bin
Toolchain version: unknown
Toolchain version: unknown
['metaligner_trimmed-trimal01-prottest_default-phyml_default']
--------------------------------------------------------------------------------
ETE build (3.1.2) - reproducible phylogenetic workflows
Citation:
Huerta-Cepas J, Serra F and Bork P. ETE 3: Reconstruction, analysis and
visualization of phylogenomic data. Mol Biol Evol (2016)
doi:10.1093/molbev/msw046
(Note that a list of the external programs used to complete all necessary
computations will be shown after workflow execution. Those programs should
also be cited.)
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
ETE build (3.1.2) - reproducible phylogenetic workflows
Citation:
Huerta-Cepas J, Serra F and Bork P. ETE 3: Reconstruction, analysis and
visualization of phylogenomic data. Mol Biol Evol (2016)
doi:10.1093/molbev/msw046
(Note that a list of the external programs used to complete all necessary
computations will be shown after workflow execution. Those programs should
also be cited.)
--------------------------------------------------------------------------------
^[[32mINFO^[[0m - Testing x86-64 portable applications...
clustalo: ^[[32mOK^[[0m - 1.2.4
dialigntx: ^[[32mOK^[[0m - This is DIALIGN-TX Version 1.0.2 - A Multiple Sequence alignment program.
fasttree: ^[[32mOK^[[0m - Usage for FastTree version 2.1.8 Double precision (No SSE3), OpenMP (2 threads):
iqtree: ^[[32mOK^[[0m - IQ-TREE multicore version 1.5.5 for Linux 64-bit built Jun 2 2017
kalign: ^[[32mOK^[[0m - Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann
mafft: ^[[32mOK^[[0m - MAFFT v6.861b (2011/09/24)
muscle: ^[[32mOK^[[0m - MUSCLE v3.8.31 by Robert C. Edgar
phyml: ^[[32mOK^[[0m - . This is PhyML version 20160115.
pmodeltest: ^[[31mMISSING^[[0m
raxml: ^[[32mOK^[[0m - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
raxml-pthreads: ^[[32mOK^[[0m - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
readal: ^[[32mOK^[[0m - readAl v1.4.rev6 build[2012-02-02]
statal: ^[[32mOK^[[0m - statAl v1.4.rev6 build[2012-02-02]
tcoffee: ^[[31mMISSING^[[0m
trimal: ^[[32mOK^[[0m - trimAl v1.4.rev6 build[2012-02-02]
^[[1;33m
WARNING: 2 external tools seem to be missing or unfunctional^[[0m
^[[1;32mInstall using conda (recomended):^[[0m
^[[0m conda install -c etetoolkit ete3_external_apps^[[0m
^[[1;32mor manually compile by running:^[[0m
^[[0m ete3 upgrade-external-tools^[[0m
clustalo: ^[[32mOK^[[0m - 1.2.4
dialigntx: ^[[32mOK^[[0m - This is DIALIGN-TX Version 1.0.2 - A Multiple Sequence alignment program.
fasttree: ^[[32mOK^[[0m - Usage for FastTree version 2.1.8 Double precision (No SSE3), OpenMP (2 threads):
iqtree: ^[[32mOK^[[0m - IQ-TREE multicore version 1.5.5 for Linux 64-bit built Jun 2 2017
kalign: ^[[32mOK^[[0m - Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann
mafft: ^[[32mOK^[[0m - MAFFT v6.861b (2011/09/24)
muscle: ^[[32mOK^[[0m - MUSCLE v3.8.31 by Robert C. Edgar
phyml: ^[[32mOK^[[0m - . This is PhyML version 20160115.
pmodeltest: ^[[31mMISSING^[[0m
raxml: ^[[32mOK^[[0m - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
raxml-pthreads: ^[[32mOK^[[0m - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
readal: ^[[32mOK^[[0m - readAl v1.4.rev6 build[2012-02-02]
statal: ^[[32mOK^[[0m - statAl v1.4.rev6 build[2012-02-02]
tcoffee: ^[[31mMISSING^[[0m
trimal: ^[[32mOK^[[0m - trimAl v1.4.rev6 build[2012-02-02]
^[[1;33m
WARNING: 2 external tools seem to be missing or unfunctional^[[0m
^[[1;32mInstall using conda (recomended):^[[0m
^[[0m conda install -c etetoolkit ete3_external_apps^[[0m
^[[1;32mor manually compile by running:^[[0m
^[[0m ete3 upgrade-external-tools^[[0m
^[[32mINFO^[[0m - Starting ETE-build execution at Sun Jul 17 22:03:04 2022
^[[32mINFO^[[0m - Output directory /home/sun/data/softwares/ete-3.1.2/ete3/tree5.1
^[[1;37;43mWRNG^[[0m - Using existing dir: /home/sun/data/softwares/ete-3.1.2/ete3/tree5.1/tmp
^[[32mINFO^[[0m - Reading nt sequences from OG0022518.all.r.fa...
^[[32mINFO^[[0m - Output directory /home/sun/data/softwares/ete-3.1.2/ete3/tree5.1
^[[1;37;43mWRNG^[[0m - Using existing dir: /home/sun/data/softwares/ete-3.1.2/ete3/tree5.1/tmp
^[[32mINFO^[[0m - Reading nt sequences from OG0022518.all.r.fa...
^[[1;37;43mWRNG^[[0m - 10 target sequences
^[[32mINFO^[[0m - ETE build starts now!
Traceback (most recent call last):
File "/home/sun/anaconda3/bin/ete3", line 33, in <module>
1,2 T sys.exit(load_entry_point('ete3==3.1.2', 'console_scripts', 'ete3')())
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete.py", line 95, in main
_main(sys.argv)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete.py", line 147, in _main
ete_build._main(arguments, builtin_apps_path)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build.py", line 1102, in _main
app_wrapper(main, args)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/interface.py", line 372, in app_wrapper
main(None, func, args)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/interface.py", line 494, in main
func(args)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build.py", line 615, in main
new_tasks = pipeline(None, wkname, config)
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/workflow/genetree.py", line 472, in pipeline
db.add_node(initial_task.threadid, initial_task.nodeid,
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/db.py", line 381, in add_node
[nodeid, cladeid, encode(targets),
File "/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/tools/ete_build_lib/db.py", line 72, in encode
return bytes.decode(base64.encodestring(six.moves.cPickle.dumps(x, 2)))
AttributeError: module 'base64' has no attribute 'encodestring'
72,2 Bot
sunny kevin
Jul 18, 2022, 8:54:18 AM7/18/22
to eteto...@googlegroups.com, dengzi...@gmail.com
Hello again,
cmd -
ete3 build -n OG0022535.all.r.fa -o tree4.1 --logfile -C 8 -w eggnog41 --clearall > tree4.1.log
After installing all the packages, ending up with this error, how do I solve this problem?
AttributeError: module 'base64' has no attribute 'encodestring'
Toolchain path: /home/sun/anaconda3/bin/ete3_apps/bin
Toolchain version: unknown['metaligner_trimmed-trimal01-prottest_default-phyml_default']
--------------------------------------------------------------------------------
ETE build (3.1.2) - reproducible phylogenetic workflows
Citation:
Huerta-Cepas J, Serra F and Bork P. ETE 3: Reconstruction, analysis and
visualization of phylogenomic data. Mol Biol Evol (2016)
doi:10.1093/molbev/msw046
(Note that a list of the external programs used to complete all necessary
computations will be shown after workflow execution. Those programs should
also be cited.)
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
ETE build (3.1.2) - reproducible phylogenetic workflows
Citation:
Huerta-Cepas J, Serra F and Bork P. ETE 3: Reconstruction, analysis and
visualization of phylogenomic data. Mol Biol Evol (2016)
doi:10.1093/molbev/msw046
(Note that a list of the external programs used to complete all necessary
computations will be shown after workflow execution. Those programs should
also be cited.)
--------------------------------------------------------------------------------
^[[32mINFO^[[0m - ETE build starts now!
Traceback (most recent call last):
File "/home/sun/anaconda3/bin/ete3", line 33, in <module>
1,2 T sys.exit(load_entry_point('ete3==3.1.2', 'console_scripts', 'ete3')())
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dengzi...@gmail.com
Jul 18, 2022, 10:04:24 AM7/18/22
to The ETE toolkit
Hi,
I'm very sorry to inform you that I noticed the ete3 package on conda channel is broken and we are working on it. Please follow the below procedure to install ete3 enviroment
#set up enviroment
conda create -n ete3 python=3.6
conda activate ete3
# install dependencies
conda install -c conda-forge pyqt
conda install six
conda install numpy
# install ete3 and toolchian
pip install ete3
conda install -c etetoolkit ete_toolchain
Ziqi
sunny kevin
Jul 18, 2022, 12:43:21 PM7/18/22
to eteto...@googlegroups.com, dengzi...@gmail.com
Hello again,
cmd -
ete3 build -n OG0022535.all.r.fa -o tree4.1.1 --logfile -C 8 -w eggnog41 --clearall > tree4.1.1.log
After reinstalling all the softwares, I ended up with the same error.
^[[32mINFO^[[0m - Starting ETE-build execution at Mon Jul 18 17:13:22 2022
^[[32mINFO^[[0m - Output directory /home/sun/data/softwares/ete-3.1.2/ete3/tree4.1.1
^[[32mINFO^[[0m - Erasing all existing npr data...
^[[32mINFO^[[0m - Reading nt sequences from OG0022535.all.r.fa...
^[[32mINFO^[[0m - Output directory /home/sun/data/softwares/ete-3.1.2/ete3/tree4.1.1
^[[32mINFO^[[0m - Erasing all existing npr data...
^[[32mINFO^[[0m - Reading nt sequences from OG0022535.all.r.fa...
^[[1;37;43mWRNG^[[0m - 10 target sequences
^[[32mINFO^[[0m - ETE build starts now!
Traceback (most recent call last):
File "/home/sun/anaconda3/bin/ete3", line 33, in <module>
To view this discussion on the web visit https://groups.google.com/d/msgid/etetoolkit/48a38ac0-1095-49a2-933a-6232ba030c9bn%40googlegroups.com.
sunny kevin
Jul 18, 2022, 12:43:21 PM7/18/22
to The ETE toolkit
Hello again,
cmd -
ete3 build -n OG0022535.all.r.fa -o tree4.1 --logfile -C 8 -w eggnog41 --clearall > tree4.1.log
After reinstalling everything, ending up with same error.
^[[32mINFO^[[0m - Starting ETE-build execution at Mon Jul 18 17:13:22 2022
^[[32mINFO^[[0m - Output directory /home/sun/data/softwares/ete-3.1.2/ete3/tree4.1.1
^[[32mINFO^[[0m - Erasing all existing npr data...
^[[32mINFO^[[0m - Reading nt sequences from OG0022535.all.r.fa...
^[[32mINFO^[[0m - Output directory /home/sun/data/softwares/ete-3.1.2/ete3/tree4.1.1
^[[32mINFO^[[0m - Erasing all existing npr data...
^[[32mINFO^[[0m - Reading nt sequences from OG0022535.all.r.fa...
^[[1;37;43mWRNG^[[0m - 10 target sequences
^[[32mINFO^[[0m - ETE build starts now!
Traceback (most recent call last):
File "/home/sun/anaconda3/bin/ete3", line 33, in <module>
dengzi...@gmail.com
Jul 18, 2022, 12:47:13 PM7/18/22
to The ETE toolkit
Hi,
this errors occur because of you are using python 3.9 which decodestring() is no longer being used. I'd reccomend you to follow the procedure I reccommended above to create an conda working enviroment of python 3.6.
Thanks!
Ziqi
sunny kevin
Jul 18, 2022, 2:11:44 PM7/18/22
to eteto...@googlegroups.com, dengzi...@gmail.com
(ete3) sun@soll:~/data/softwares/ete-3.1.2/ete3$ python --version
Python 3.6.13 :: Anaconda, Inc.
Suggestions please!
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sunny kevin
Jul 18, 2022, 2:11:44 PM7/18/22
to The ETE toolkit
(ete3) sun@soll:~/data/softwares/ete-3.1.2/ete3$ python --version
Python 3.6.13 :: Anaconda, Inc.
Python 3.6.13 :: Anaconda, Inc.
ziqi deng
Jul 18, 2022, 2:29:11 PM7/18/22
to eteto...@googlegroups.com
I see the problem now,
I'm afraid that I have to correct the procedure above in regards to install ete3.
I found the ete3.1.2 from another channel which should be able to work
conda install -c conda-forge ete3
But before you may have to pip uninstall ete3 first. Thanks for your patience
Ziqi
sunny kevin <sunnyk...@gmail.com> 于2022年7月18日周一 20:11写道：
To view this discussion on the web visit https://groups.google.com/d/msgid/etetoolkit/d12a488b-2583-43d3-a040-98b7208fb1a2n%40googlegroups.com.
sunny kevin
Jul 19, 2022, 4:35:41 AM7/19/22
to eteto...@googlegroups.com, dengzi...@gmail.com
HI ,
Trying to run the program with 10 cpus, running from the past ~4 days only 158 /2000 orthologs were computed ?
How do I increase the speed, Suggestions please, I had lots of datasets to compute.
Trying to run the program with 10 cpus, running from the past ~4 days only 158 /2000 orthologs were computed ?
How do I increase the speed, Suggestions please, I had lots of datasets to compute.
CMD-
ete3 evol -t OG369.treefile --alg ${i} -o ${i}.allsites --models M0 M1 M2 M3 M4 M5 M6 M7 M8 M8a --cpu 10 --slr_binary /home/sun/data/softwares/slr/slr/bin > ${i}.Ete3.log
Warning, what I'd be the reason ??
/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/evol/evoltree.py:537: UserWarning:
WARNING: Likelihood of the alternative model is smaller than null's (-2625.971095 - -2625.971138 = 0.000043)
Best,
K
ete3 evol -t OG369.treefile --alg ${i} -o ${i}.allsites --models M0 M1 M2 M3 M4 M5 M6 M7 M8 M8a --cpu 10 --slr_binary /home/sun/data/softwares/slr/slr/bin > ${i}.Ete3.log
Warning, what I'd be the reason ??
/home/sun/anaconda3/lib/python3.9/site-packages/ete3-3.1.2-py3.9.egg/ete3/evol/evoltree.py:537: UserWarning:
WARNING: Likelihood of the alternative model is smaller than null's (-2625.971095 - -2625.971138 = 0.000043)
Best,
K
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