Unable to run medaka_consensus on Mac M3

[sandeepkasaragod]

I am running medaka_consensus on MacBook M3 pro. The commands are as follows.

medaka consensus --model r941_min_fast_g303 \
--threads 5 \
--chunk_len 800 \
--chunk_ovlp 400 \
--RG 1 /projects/Artic_testing_Feb5/Artic-nf/results/medaka/NTC1.trimmed.rg.sorted.bam /projects/Artic_testing_Feb5/Artic-nf/results/medaka/NTC1.1.hdf 

I get following error message zsh: illegal hardware instruction medaka consensus --model r941_min_fast_g303 --threads 5 --chunk_len 800 400

I also tried running medaka_consensus which just prints the message mentioned below

TF_CPP_MIN_LOG_LEVEL is set to '3'

[cjw85]

The error

illegal hardware instruction

suggests to me that you are using code compiled for x86 on your ARM-based macBook. How did you install medaka?

[sandeepkasaragod]

Thanks Chris for your message.

I have installed it from the custom yml file.

name: artic_nf channels:

• conda-forge
• bioconda
• defaults dependencies:
• nextflow
• artic

CONDA_SUBDIR=osx-64 mamba env create -f environment.yml conda activate artic_nf conda config --env --set subdir osx-64

The Medaka is downloaded from the artic package

[cjw85]

We do not maintain or support the use of bioconda packages. To my knowledge bioconda does not build ARM packages. I don't know what you have done to your system to coerce it to install the x86 conda package but it should not be possible.

To use medaka on macOS you will need to compile it from source as we do not distribute a binary package.

[sandeepkasaragod]

Thank you for the solution. Let me try compiling medaka.

[cjw85]

Running pip install medaka even on your Mac should suffice provided your computer has all the necessary tools installed to compile the code. Alternatively checkout the git repository and follow the instructions in the README.