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moold avatar moold commented on June 13, 2024

Please check the default python version, NextPolish only works with python 2.7.

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berombau avatar berombau commented on June 13, 2024

After the make installation, I changed the hashbang of the nextPolish executable to /data/dp1/local/miniconda3/envs/nextpolish/bin/python
It points to a Python environment created with:

conda create -n nextpolish python=2.7 psutil

(nextpolish) berombau@agro:/data/dp1/public/short-reads$ /data/dp1/local/miniconda3/envs/nextpolish/bin/python --version
Python 2.7.15
(nextpolish) berombau@agro:/data/dp1/public/short-reads$ conda list
# packages in environment at /data/dp1/local/miniconda3/envs/nextpolish:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main    conda-forge
ca-certificates           2019.11.28           hecc5488_0    conda-forge
certifi                   2019.11.28               py27_0    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 9.2.0                hdf63c60_0    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_0    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
openssl                   1.1.1d               h516909a_0    conda-forge
pip                       19.3.1                   py27_0    conda-forge
psutil                    5.6.7            py27h516909a_0    conda-forge
python                    2.7.15            h5a48372_1009    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
setuptools                42.0.2                   py27_0    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
wheel                     0.33.6                   py27_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge

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moold avatar moold commented on June 13, 2024

May be you need change the python in /data/dp1/public/output/nextpolish/01_rundir/00.score_chain/04.polish.ref.sh.work/polish_genome00/nextPolish.sh to /data/dp1/local/miniconda3/envs/nextpolish/bin/python, or add /data/dp1/local/miniconda3/envs/nextpolish/bin/python to your environment, so when you run python, it call the /data/dp1/local/miniconda3/envs/nextpolish/bin/python.

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berombau avatar berombau commented on June 13, 2024

An incorrect version of python was indeed the problem. I solved my error by activating the conda environment and executing the unaltered executable with python directly:

conda activate nextpolish
python {path_to_nextPolish} run.cfg

Thank you for your help!

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