The issues arise while installing the libraries

[A. A. K. Prabhath Amarasinghe]

I installed the older version (2.7.18) of python and tried to install libraries required for the analysis. I was able to install other libraries except PyTables, although it gives a message "DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.". When I was trying to install the PyTables, an error message appeared like this, "ERROR: Command errored out with exit status 1: 'C:\Python27\python.exe' 'C:\Python27\lib\site-packages\pip' install --ignore-installed --no-user --prefix 'c:\users\kanchana\appdata\local\temp\pip-build-env-76spjt\overlay' --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel oldest-supported-numpy Check the logs for full command output." 

In my computer I have installed both python 2.7.18, python 3.10 with all required libraries, and the latest Anaconda version. I tried with all this application to run your software and I failed to obtain successful results. When I tried to deal with python 3.10 and Anaconda 3(Anaconda prompt) an error came like this in both situations, "python C:\partitionfinder-2.1.1\PartitionFinder.py C:\partitionfinder-2.1.1\examples\nucleotide

Traceback (most recent call last):
  File "C:\partitionfinder-2.1.1\PartitionFinder.py", line 21, in <module>
    from partfinder import main
  File "C:\partitionfinder-2.1.1\partfinder\main.py", line 23, in <module>
    import logtools
ModuleNotFoundError: No module named 'logtools' ".

Still I am a beginner in bioinformatics and I have some sort of basic knowledge on python. If someone would guide me to overcome this, I would be much obliged to you and grateful. 

Thank You

[Rob Lanfear]

Hi there,

PartitionFinder is getting a bit old and hard to use now. So my suggestion is to move to iqtree2, and use ModelFinder instead. 

Just scroll down to "choosing the right partitioning scheme" here: http://www.iqtree.org/doc/Advanced-Tutorial

Rob

[A. A. K. Prabhath Amarasinghe]

I managed to install an Anaconda older version and all the things were done pretty well. I copied the partitioning details (Bayesian block) directly into the alignment file to construct the Cladogram using MrBayes. Is that the correct way to feed the partitioning details for subsequent analysis?

Note: Anyone can use this link to download the any version of anaconda:- https://repo.anaconda.com/archive/

cheers

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Mr. Prabhath Amarasinghe | 

BSc. (Hons.),

Research Assistant,
Department of Parasitology,

Faculty of Medicine,
University of Jaffna,
Sri Lanka.