Hello,
I've been trying to install QIIME2 on my new mac (M2 Pro chip, macOS 13.2.1) and I am having issues. I saw similar posts about issues using M1 macs, but my issue seems to be different.
I first tried installing with Miniconda (conda version 23.3.1), which I also just installed today, and I followed the instructions here for installing qiime2 for MacOS (Apple Silicon). I ran into an error at the end of the download, which I will reproduce below. After reading some of the other QIIME2 forum downloading errors, I tried removing my QIIME2 environment and un-installing Miniconda, then installing Anaconda3 (conda version 23.3.1) and trying the QIIME2 download again. I tried both the MacOS (Apple Silicon) and the MacOS (Intel) versions, removing the qiime2 conda environment directories between each attempt, and nothing has worked.
Here are my current versions of each program:
python --version
Python 3.10.9
conda --version
conda 23.3.1
wget --version
GNU Wget 1.21.3 built on darwin20.0.0.
I ran the following commands (note that I simplified the name of my environment to qiime2):
conda install wget
wget https://data.qiime2.org/distro/core/qiime2-2023.2-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2 --file qiime2-2023.2-py38-osx-conda.yml
conda activate qiime2-2023.2
^ Creating the environment is where it fails each time. It downloaded everthing successfully, and almost finished, but I always run into this error at the end (same error for Miniconda vs. Conda, and Intel vs. Silicon versions):
Collecting package metadata (repodata.json): done
Solving environment: done
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(740): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'.
Rolling back transaction: done
LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0
location of failed script: /Users/brookeweigel/anaconda3/envs/qiime2/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
==> script output <==
stdout:
stderr: /Users/brookeweigel/anaconda3/envs/qiime2/bin/tab-qiime: /Users/brookeweigel/anaconda3/envs/qiime2/bin/qiime: /Users/brookeweigel/anaconda3/envs/qiime2/bin/python: bad interpreter: Bad CPU type in executable
++ dirname -- /Users/brookeweigel/anaconda3/envs/qiime2/bin/installBiocDataPackage.sh
- SCRIPT_DIR=/Users/brookeweigel/anaconda3/envs/qiime2/bin/../share/bioconductor-data-packages
- json=/Users/brookeweigel/anaconda3/envs/qiime2/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.9".fn' /Users/brookeweigel/anaconda3/envs/qiime2/bin/../share/bioconductor-data-packages/dataURLs.json
/Users/brookeweigel/anaconda3/envs/qiime2/bin/installBiocDataPackage.sh: /Users/brookeweigel/anaconda3/envs/qiime2/bin/yq: /Users/brookeweigel/anaconda3/envs/qiime2/bin/python3.8: bad interpreter: Bad CPU type in executable - FN=
return code: 126
()
I'm still able to activate my qiime2 environment with "conda activate qiime2" but it does not work.
When I run "qiime --help" it says "zsh: command not found: qiime"
Please help! I've been a qiime2 user for a long time, and I would really like to run it on my new mac soon to analyze some exciting data! Thank you!