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WGLab / RepeatHMM

a hidden Markov model to infer simple repeats from genome sequences
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No module named 'UnsymmetricPairAlignment #51

Closed ghost closed 2 years ago

ghost commented 2 years ago

when run the RepeatHMM software, python ./bin/repeatHMM.py , show the error message :

image

Installation process： source activate RepeatHMM

  1. Download RepeatHMM git clone https://github.com/WGLab/RepeatHMM
  2. Create conda environment. cd RepeatHMM conda env create -f environment.yml source activate repeathmmenv cd bin/RepeatHMM_scripts/UnsymmetricPairAlignment make cd ../../../
liuqianhn commented 2 years ago

@huangrongbioinfomation "UnsymmetricPairAlignment" is under "bin/RepeatHMM_scripts/UnsymmetricPairAlignment". Could you please show you have under 'bin/RepeatHMM_scripts/UnsymmetricPairAlignment/'? Meanwhile, I see 'base' conda environment is used in the screenshot. Please 'source activate repeathmmenv' or 'conda activate repeathmmenv' each time when you use RepeatHMM.

Meanwhile, you can try the command below under bin/RepeatHMM_scripts/UnsymmetricPairAlignment, and bin/RepeatHMM_scripts, and share what is the output

under bin/RepeatHMM_scripts/UnsymmetricPairAlignment: after type python, then, import UnsymmetricPairAlignment

under bin/RepeatHMM_scripts/: after type python, then, from UnsymmetricPairAlignment import UnsymmetricPairAlignment

ghost commented 2 years ago

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