Issue with Running Strainy - ModuleNotFoundError: No module named 'flye.six.moves'

[GuillermoIllan]

Dear maintainers,

I encountered an issue while trying to run the strainy program after following the installation instructions provided in the repository. Below are the steps I followed:

git clone https://github.com/katerinakazantseva/strainy cd strainy git submodule update --init make -C submodules/Flye conda env create -f environment.yml -n strainy

However, when I attempt to run the program using the command ./strainy.py -h, I receive the following error:

Matplotlib is building the font cache; this may take a moment. Traceback (most recent call last): File "/home/guillermo/software/strainy/./strainy.py", line 29, in <module> main() File "/home/guillermo/software/strainy/./strainy.py", line 24, in main import strainy.main File "/home/guillermo/software/strainy/strainy/main.py", line 11, in <module> from strainy.phase import phase_main File "/home/guillermo/software/strainy/strainy/phase.py", line 15, in <module> from strainy.flye_consensus import FlyeConsensus File "/home/guillermo/software/strainy/strainy/flye_consensus.py", line 22, in <module> from flye.main import _run_polisher_only File "/home/guillermo/software/strainy/submodules/Flye/flye/main.py", line 19, in <module> import flye.polishing.alignment as aln File "/home/guillermo/software/strainy/submodules/Flye/flye/polishing/alignment.py", line 18, in <module> import flye.utils.fasta_parser as fp File "/home/guillermo/software/strainy/submodules/Flye/flye/utils/fasta_parser.py", line 26, in <module> from flye.six.moves import range ModuleNotFoundError: No module named 'flye.six.moves'

It seems that there is an issue with the Flye submodule, specifically a missing module flye.six.moves.

Could you please provide guidance on how to resolve this issue?

Thank you for your help and for maintaining this project!

Best regards, Guillermo Illan

[mikolmogorov]

Hello,

This is due to Flye failing to install with Python 3.12: https://github.com/mikolmogorov/Flye/issues/669. The best solution for now is using an earlier version of python - or alternatively try the provided docker container. We are aiming to fix this in the future on the Flye side.

[mikolmogorov]

In fact, just pushed an update - I think it should work with 3.12 now.

[GuillermoIllan]

In fact, just pushed an update - I think it should work with 3.12 now.

Thank you so much! The problem is solved and strainy is working properly.