Issue with downloading QIIME2

User Support
1

Hello! I am trying to download QIIME2 on my MacBook (M3 silicon chip) using this code:

CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-osx-conda.yml
conda activate qiime2-metagenome-2024.10
conda config --env --set subdir osx-64

However, I received an error when downloading it and I am not sure how to fix it.

(base) anndonxlow@Lows-Laptop ~ % CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-osx-conda.yml
conda activate qiime2-amplicon-2024.10
conda config --env --set subdir osx-64
/Users/anndonxlow/miniconda3/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
  action(self, namespace, argument_values, option_string)
Channels:
 - https://packages.qiime2.org/qiime2/2024.10/amplicon/released
 - conda-forge
 - bioconda
 - qiime2
 - defaults
Platform: osx-64
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(951): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1'.
Rolling back transaction: done

LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1
location of failed script: /Users/anndonxlow/miniconda3/envs/qiime2-amplicon-2024.10/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: 
stderr: /Users/anndonxlow/miniconda3/envs/qiime2-amplicon-2024.10/bin/tab-qiime: /Users/anndonxlow/miniconda3/envs/qiime2-amplicon-2024.10/bin/qiime: /Users/anndonxlow/miniconda3/envs/qiime2-amplicon-2024.10/bin/python: bad interpreter: Bad CPU type in executable
++ dirname -- /Users/anndonxlow/miniconda3/envs/qiime2-amplicon-2024.10/bin/installBiocDataPackage.sh
+ SCRIPT_DIR=/Users/anndonxlow/miniconda3/envs/qiime2-amplicon-2024.10/bin/../share/bioconductor-data-packages
+ json=/Users/anndonxlow/miniconda3/envs/qiime2-amplicon-2024.10/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.11".fn' /Users/anndonxlow/miniconda3/envs/qiime2-amplicon-2024.10/bin/../share/bioconductor-data-packages/dataURLs.json
/Users/anndonxlow/miniconda3/envs/qiime2-amplicon-2024.10/bin/installBiocDataPackage.sh: /Users/anndonxlow/miniconda3/envs/qiime2-amplicon-2024.10/bin/yq: /Users/anndonxlow/miniconda3/envs/qiime2-amplicon-2024.10/bin/python3.10: bad interpreter: Bad CPU type in executable
+ FN=

return code: 126

()

I do see an environment name ((qiime2-amplicon-2024.10) ) on my terminal. However, when I try to run this code, it says QIIME is not available:

(qiime2-amplicon-2024.10) anndonxlow@Lows-Laptop ~ % qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path /Users/anndonxlow/Desktop/manifest.tsv \
  --input-format PairedEndFastqManifestPhred33V2 \
  --output-path /Users/anndonxlow/Desktop/demux.qza
zsh: command not found: qiime

Any help on this issue will be appreciated. Thank you.

2

Hey @anndonxlow,

It looks like our rather classic post-link (post install really) error from genomeinfodbdata. This is where it downloads a reference database, and once in a while the server hosting the data will hiccup causing the environment to not finish its setup.

You should be able to start over with the environment creation and cross your fingers that it doesn't happen twice in a row.

4 Likes
3

I have found the latest Qiime2 Docker image very useful. Give it a go!

2 Likes