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Psy-Fer / SquiggleKit

SquiggleKit: A toolkit for manipulating nanopore signal data
MIT License
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unable to plot individual .fast5 after installing vbz plugin #58

Open emmarl25 opened 2 years ago

emmarl25 commented 2 years ago

I'm trying to run SquigglePlot on an individual .fast5 file on my Mac. Though the plot shows up, I don't see any current output; instead, I keep getting the error OSError: Can't read data (can't open directory: /opt/homebrew/Caskroom/miniforge/base/lib/hdf5/plugin). I then installed the vbz_compression plugin from ont-vbz through the following package listed in the installers: ont-vbz-hdf-plugin-1.0.1-Darwin.pkg. However, this still hasn't fixed the issue. I would appreciate any help.

Thanks, Emma

Psy-Fer commented 2 years ago

Hello Emma,

When you say it "still hasn't fixed the issue", do you mean you are still getting the same OSError? Are you running everything in an environment?

Please try reinstalling the libraries, specifically h5py. 

pip remove h5py
pip install h5py

Let me know if that helps

James

emmarl25 commented 2 years ago

I removed and re-installed h5py via pip uninstall h5py and pip install h5py. However, when I went back and tried python SquigglePlot.py -i /data/.fast5, I still received the following error...

Screen Shot 2022-09-26 at 12 40 28 AM
Psy-Fer commented 2 years ago

Ahh, i see. Your mac has an ARM64 processor and you installed an x86_64 install

Please remove the VBZ version you installed, and re-install an ARM compatible version.

For example, this one. https://github.com/nanoporetech/vbz_compression/releases/download/1.0.2/ont-vbz-hdf-plugin-1.0.2-Darwin-arm64.pkg

Note the -arm64 at the end.

Then re-install h5py and see if that works.

James