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WGLab / RepeatHMM

a hidden Markov model to infer simple repeats from genome sequences
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ImportError: No module named _UnsymmetricPairAlignment #32

Closed Tine-dk closed 4 years ago

Tine-dk commented 4 years ago

Hi. I followed the installation guide but I get this error when running the software: ImportError: No module named _UnsymmetricPairAlignment

But I do have something called _UnsymmetricPairAlignment.cpython-37m-x86_64-linux-gnu.so under /RepeatHMM/bin/RepeatHMM_scripts/UnsymmetricPairAlignment.

I'm not sure how to solve the error. Any suggestion is very appreciated. :)

liuqianhn commented 4 years ago

@Tine-dk Do you do the following steps

cd bin/scripts/UnsymmetricPairAlignment
make

If yes, could you please show me what are under RepeatHMM/bin/RepeatHMM_scripts/UnsymmetricPairAlignment?

Meanwhile, which python are you use for repeatHMM?

Tine-dk commented 4 years ago

Yes, I did that step. The Python version in the environment I created is 2.7.18. Is that alright?

Under the folder "UnsymmetricPairAlignment" there is the following content: init.py init.pyc _UnsymmetricPairAlignment.cpython-37m-x86_64-linux-gnu.so Makefile setup.py UnsymmetricPairAlignment.c UnsymmetricPairAlignment.i UnsymmetricPairAlignent.py UnsymmetricPairAlignment.pyc UnsymmetricPairAlignment_wrap.c build/temp.linux-x86_64-3.7/UnsymmetricPairAlignment.o build/temp.linux-x86_64-3.7/UnsymmetricPairAlignment_wrap.o

liuqianhn commented 4 years ago

It seems that your compilation results are different from mine: I have _UnsymmetricPairAlignment.so rather than _UnsymmetricPairAlignment.cpython-37m-x86_64-linux-gnu.so. Could you please rename your .so file to see what happen? I do not know why you have the different file now.

Tine-dk commented 4 years ago

I renamed the file but unfortunately, it does not solve the error.

ImportError: /RepeatHMM/bin/RepeatHMM_scripts/UnsymmetricPairAlignment/_UnsymmetricPairAlignment.so: undefined symbol: PyUnicode_FromFormat

Tine-dk commented 4 years ago

I think I solved it. It was the order I did the installation steps in. If the UnsymmetricPairAlignment has been "made" before the environment has been created and activated, the error occurs. Now I have the correct .so file.