CAMISIM: Getting it to run locally

[ndreey]

I will post logs of error management.

Good to know

• Running Ubuntu 20.04 LTS on WSL2 (Windows 11 Laptop)

• Created a conda environment CAMISIM where i installed the required dependencies for metagenomesimulation.py

  • conda create -n CAMISIM python=3
  • conda install biopython
  • numpy
  • .matplotlib
  • sudo apt-get install perl perl
  • sudo apt-get install libxml-simple-perl
  • conda config --add channels bioconda
  • conda config --add channels conda-forge
  • conda install samtools

• Cloned CAMISIM

  • git clone https://github.com/CAMI-challenge/CAMISIM

• Test run with the default/ files

  • conda install joblib
  • conda install scipy
  • conda install scikit-learn-intelex

• the env CAMISIM was running python 3.11.0

  • This caused an error
    • ImportError: cannot import name 'Iterable' from 'collections'
  • changing from collections import Iterable to:
    • from collections.abc import Iterable in:
    • CAMISIM/scripts/configparserwrapper.py fixed this issue.
  • Python > 3.9 removed the Iterable from collections module.
    • it however caused errors downstream so i reverted back to from collections import Iterable and downgraded python.
  • Downgraded python to 3.9
    • conda install python=3.9 and downgraded all the packages when prompted.

• It is now letting me run the simulation but i am getting this error.

  • /mnt/c/Users/andbo/thesis_andbo/CAMISIM/tools/samtools-1.3/samtools: error while loading shared libraries: libncursesw.so.5: cannot open shared object file: No such file or directory
  • The output folder with the subfolders are created but nothing is stored in there.
  • tested reinstalling libncursesw5 but nothing worked

to be continued... CAMISIM_ERROR_LOG.txt

[ndreey]

FIXED!!

• Uninstalled env CAMISIM
  • conda env remove --name CAMISIM
• conda create --name thesis_CAMISIM python=3.9
• conda install biopython numpy matplotlib joblib scipy ncurses
• Got same error when running metagenomesimulation.py
  • /CAMISIM/tools/samtools-1.3/samtools: error while loading shared libraries: libncursesw.so.5: cannot open shared object file: No such file or directory
• Started new WSL terminal, and moved to /home/PATH/lib
  • find . -name libncursesw.so.5 gave nothing
  • sudo apt-get install libncursesw5
• Test ran in terminal with the env thesis_CAMISIM activated and it worked.
  • python3 metagenomesimulation.py defaults/mini_config.ini

Waiting for the run to finish, but the out/ is 1GB large now so seems to be working. Will close the issue if this run is successful.

It worked!