Chris Seymour

I see the issue - `mappy` doesn't provide precompiled wheels https://github.com/lh3/minimap2/issues/449. It's compiled on your system at install time and requires the zlib headers. > python/cmappy.h:6:18: fatal error: zlib.h: No...

@madhubioinfo it's not clear to me this failed. Can you try `bonito -v` now?

@madhubioinfo see https://github.com/nanoporetech/bonito/issues/260 - can you downgrade `protobuf` and check `bonito -v` shows `0.5.3`. ``` $ pip install protobuf==3.20.1 $ bonito -v ```

What GPU and driver version do you have? Can you provide the output from `nvidia-smi`?

Hey @AzlanNI I am seeing a mixed of `python3.6` and `python3.7` in your output and `python3.6` is end of life. Are you able to create a new `python3.7` virtual environment...

Can you try.. ``` (venv3.7) $ deactivate $ rm -rf venv3.7 $ python3.7 -m venv venv3.7 $ source ./venv3.7/bin/activate $ python3.7 -m pip install --upgrade pip $ python3.7 -m pip...

Dataclasses are Python3.7+ feature and the output shows that `.local/lib/python3.6/site-packages/` is still getting picked up. ``` File "/home/azlan/.local/lib/python3.6/site-packages/dataclasses.py", line 958, in dataclass return wrap(_cls) File "/home/azlan/.local/lib/python3.6/site-packages/dataclasses.py", line 950, in wrap...

Where did you get this build of Python 3.7 from? It's missing `bz2` support - see https://stackoverflow.com/questions/12806122/missing-python-bz2-module

Each models default configuration will use around 11GB of GPU memory but you can reduce the `batchsize` to use less. Add `-v` to `bonito basecaller` to see what the default...

Hey @wharvey31 Bonito doesn't currently support multi-gpu calling and the behaviour you are seeing is the default for frameworks like PyTorch and TensorFlow. You can manage which devices are available...