Error to run PF2
Juan Esteban Uribe Arboleda
MacBook-Pro-de-juan:~ JuanEs$ Python /Users/JuanEs/Desktop/Pleurotomarioidea/Matrices/partitionfinder-2.1.1/PartitionFinder.py /Users/JuanEs/Desktop/Pleurotomarioidea/Matrices/partitionfinder-2.1.1/examples/nucleotide/partition_finder.cfg
Traceback (most recent call last):
File "/Users/JuanEs/Desktop/Pleurotomarioidea/Matrices/partitionfinder-2.1.1/PartitionFinder.py", line 21, in <module>
from partfinder import main
File "/Users/JuanEs/Desktop/Pleurotomarioidea/Matrices/partitionfinder-2.1.1/partfinder/main.py", line 23, in <module>
import logtools
ImportError: No module named 'log tools'
What could I do?
all the best
Juanes
Paul Frandsen
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composed on my phone, apologies for any typos
Rob Lanfear
Hi Juanes,
I think Paul has hit the nail on the head. In case he's right, here's an explanation which should get you up and running.
It looks from this (though it’s very hard for you to know that from the output, which I’ll work on) that you’re using Python 3.x not Python 2.7.x.
Things to do:
- Check with version of Python you get when you just type ‘python’ at the commandline like this:
python --version
- You should get something that says Python 2.7.something, like this
aquila:~ roblanfear$ python --version
Python 2.7.12 :: Anaconda custom (x86_64)
If you do, then I’m wrong about the problem, so post and let me know.
If you get something else, perhaps like this:
(snakes) aquila:~ roblanfear$ python --version
Python 3.5.2 :: Continuum Analytics, Inc.
then you are using the wrong version of Python. This can happen even if you followed the setup instructions, if you have previously installed Python 3.x and have your system set up to default to that.
The simplest fix here is to just set up a Python environment for Python 2, and run PartitionFinder from that environment. Here’s how to do that (details here: http://conda.pydata.org/docs/using/envs.html):
# create a python 2 environment
conda create --name python2 python=2
# activate that environment
source activate python2
# the new environment won't have the dependencies you need, but installing them once is all you need. Just say 'yes' to installing them when prompted
conda install numpy pandas pytables pyparsing scipy scikit-learn
# now check that you get python 2.7.x when you type Python
python --version
As long as you get output that says ‘python 2.7.something’ in the last step, you can then run PartitionFinder2 from that environment, with your commandline as before:
Python /Users/JuanEs/Desktop/Pleurotomarioidea/Matrices/partitionfinder-2.1.1/PartitionFinder.py /Users/JuanEs/Desktop/Pleurotomarioidea/Matrices/partitionfinder-2.1.1/examples/nucleotide/partition_finder.cfg
Once your analysis is done, you can get out of that environment by typing
source deactivate
or just closing your terminal window.
To keep using the setup like this, you just type
source activate python2
before running your PF2 analyses in future. This will load the environment you need, with all the packages you already installed. I.e. once you activate the environment, you can just go ahead an run PF2.
Please let me know if this works - if it does, I’ll add a more useful error message to PF2 to this effect.
Cheers,
Rob
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Ecology, Evolution, and Genetics,
Christopher Smith
(python2) MacBook-Pro-18:~ chrissmith$ python /Applications/partitionfinder-2.1.1/PartitionFinder.py /Applications/partitionfinder-2.1.1/examples/nucleotide
**** ERROR ****
Could not find the dependency numpy, please check that you have followed the installation instructions in the manual and try again.
PartitionFinder 2 (unlike PartitionFinder 1) requires a few other Python packages to work. All of these can be installed very easily, in a single click, by installing the Python 2.7.x version of the Anaconda Python distrubition, which you can find here (remember to get the 2.7 version!):
https://www.continuum.io/downloads
Further instructions are in the installation section of the manual, which points out a number of other differences between PartitionFinder 1 and PartitionFinder 2 too.
***************
Traceback (most recent call last):
File "/Applications/partitionfinder-2.1.1/PartitionFinder.py", line 20, in <module>
from partfinder import dependencies
File "/Applications/partitionfinder-2.1.1/partfinder/dependencies.py", line 43, in <module>
raise ImportError
ImportError
(python2) MacBook-Pro-18:~ chrissmith$ conda create --name python2 python=2.7
CondaValueError: prefix already exists: /anaconda3/envs/python2
(python2) MacBook-Pro-18:~ chrissmith$ python --version
Python 2.7.14 :: Anaconda, Inc.
(python2) MacBook-Pro-18:~ chrissmith$
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Rob Lanfear
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Division of Ecology and Evolution,