I have a problem with install qiime2 on M1 mac using miniconda3

Hello. I am Juneyoung from South Korea.

I try to install qiime2 2022.2 version on my M1 macbook.
But I have some error message from the terminal.

  • Here is the message from the terminal.
    (base) [email protected] ~ % conda env create -n qiime2-2022.2 --file qiime2-2022.2-py38-osx-conda.yml
    Collecting package metadata (repodata.json): done
    Solving environment: failed

ResolvePackageNotFound:

  • q2-types=2022.2.0
  • gfortran_osx-64=9.3.0
  • blast=2.12.0
  • r-rcurl=1.98_1.6
  • q2templates=2022.2.0
  • scikit-bio=0.5.6
  • gfortran_impl_osx-64=9.3.0
  • q2-feature-table=2022.2.0
  • bowtie2=2.4.5
  • bioconductor-iranges=2.28.0
  • fasttree=2.1.10
  • q2-feature-classifier=2022.2.0
  • bioconductor-zlibbioc=1.40.0
  • pbzip2=1.1.13
  • perl-compress-raw-zlib=2.101
  • bioconductor-rsamtools=2.10.0
  • perl-json-xs=2.34
  • q2-mystery-stew=2022.2.0
  • q2-deblur=2022.2.0
  • perl-encode=3.16
  • q2-metadata=2022.2.0
  • mafft=7.490
  • qiime2=2022.2.0
  • raxml=8.2.12
  • perl-pathtools=3.75
  • cutadapt=3.5
  • q2-diversity-lib=2022.2.0
  • vsearch=2.7.0
  • bioconductor-genomicranges=1.46.0
  • q2-alignment=2022.2.0
  • q2-taxa=2022.2.0
  • q2-quality-control=2022.2.0
  • q2-emperor=2022.2.0
  • q2-composition=2022.2.0
  • sepp=4.3.10
  • r-jpeg=0.1_9
  • q2galaxy=2022.2.0
  • perl-compress-raw-bzip2=2.101
  • sortmerna=2.0
  • libgfortran5=9.3.0
  • perl-scalar-list-utils=1.61
  • bioconductor-shortread=1.52.0
  • q2-vsearch=2022.2.0
  • bioconductor-rhtslib=1.26.0
  • python-isal=0.11.1
  • pandoc=2.17.1.1
  • bioconductor-s4vectors=0.32.0
  • bioconductor-xvector=0.34.0
  • q2-quality-filter=2022.2.0
  • iqtree=2.2.0_beta
  • bioconductor-biostrings=2.62.0
  • q2-sample-classifier=2022.2.0
  • q2-demux=2022.2.0
  • bioconductor-delayedarray=0.20.0
  • q2-cutadapt=2022.2.0
  • q2-fragment-insertion=2022.2.0
  • bioconductor-dada2=1.22.0
  • q2-diversity=2022.2.0
  • xopen=1.4.0
  • r-rcppparallel=5.1.5
  • q2-phylogeny=2022.2.0
  • isa-l=2.30.0
  • emperor=1.0.3
  • unifrac=0.20.3
  • htslib=1.14
  • q2cli=2022.2.0
  • dnaio=0.7.1
  • samtools=1.14
  • perl-list-moreutils-xs=0.430
  • hmmer=3.1b2
  • bioconductor-biocparallel=1.28.0
  • bioconductor-genomicalignments=1.30.0
  • perl-io-compress=2.102
  • q2-gneiss=2022.2.0
  • q2-longitudinal=2022.2.0
  • r-bitops=1.0_7
  • bioconductor-biobase=2.54.0
  • entrez-direct=16.2
  • biom-format=2.1.10
  • r-vegan=2.5_7
  • libimagequant=2.17.0
  • q2-dada2=2022.2.0
  • libgcc=4.8.5

(base) [email protected] ~ %

  • My conda info is this.
    (base) [email protected] ~ % conda info

    active environment : base
    active env location : /Users/juneyoung/miniconda3
    shell level : 1
    user config file : /Users/juneyoung/.condarc
    populated config files : /Users/juneyoung/.condarc
    conda version : 4.12.0
    conda-build version : not installed
    python version : 3.8.13.final.0
    virtual packages : __osx=12.3.1=0
    __unix=0=0
    __archspec=1=arm64
    base environment : /Users/juneyoung/miniconda3 (writable)
    conda av data dir : /Users/juneyoung/miniconda3/etc/conda
    conda av metadata url : None
    channel URLs : conda-forge/osx-arm64
    conda-forge/noarch
    https://conda.anaconda.org/bioconda/osx-arm64
    bioconda/noarch
    main/osx-arm64
    main/noarch
    https://repo.anaconda.com/pkgs/r/osx-arm64
    r/noarch
    package cache : /Users/juneyoung/miniconda3/pkgs
    /Users/juneyoung/.conda/pkgs
    envs directories : /Users/juneyoung/miniconda3/envs
    /Users/juneyoung/.conda/envs
    platform : osx-arm64
    user-agent : conda/4.12.0 requests/2.27.1 CPython/3.8.13 Darwin/21.4.0 OSX/12.3.1
    UID:GID : 501:20
    netrc file : None
    offline mode : False

I deleted the miniconda3 three times and repeat again on Natively installing QIIME 2 — QIIME 2 2022.2.0 documentation

Can you help me for installing the qiime2 on my mac?

Also, I am trying to this post (Install QIIME2 on Macbook Pro 2021 with apple M1 Chip)

(base) [email protected] ~ % CONDA_SUBDIR=osx-64 conda env create -n qiime2-2022.2 --file qiime2-2022.2-py38-osx-conda.yml

Collecting package metadata (repodata.json): done

Solving environment: -

Found conflicts! Looking for incompatible packages.

This can take several minutes. Press CTRL-C to abort.

Hi @Juneyoung_Lee, welcome to :qiime2:!

In order to install and run conda & QIIME on an M1 mac you need to select the Terminal application, then press Command-I, to bring up the Terminal application information window. Check the box "Open using Rosetta". Then close / restart the Terminal app if needed.

Then install the regular version of OS X conda, not the M1 version. then everything should work as expected. At least this is all I needed to do to get it working on my laptop.

-Mike

2 Likes

@SoilRotifer I'm getting the same issue though on a 2019 Mac Pro with the Intel processor. I am using my (updated) existing anaconda build. Is that likely to cause a problem?

Hard to say unless I can see the error messages. If you are seeing osx-arm64 or something similar in your error messages, then you've simply installed the wrong version of conda.

(base) [email protected] ~ % conda info

 active environment : base
active env location : /Users/juneyoung/miniconda3
        shell level : 1
   user config file : /Users/juneyoung/.condarc

populated config files : /Users/juneyoung/.condarc
conda version : 4.12.0
conda-build version : 3.21.8
python version : 3.9.12.final.0
virtual packages : __osx=12.3.1=0
__unix=0=0
__archspec=1=x86_64
base environment : /Users/juneyoung/miniconda3 (writable)
conda av data dir : /Users/juneyoung/miniconda3/etc/conda
conda av metadata url : None
channel URLs : conda-forge/osx-64
conda-forge/noarch
bioconda/osx-64
bioconda/noarch
main/osx-64
main/noarch
r/osx-64
r/noarch
package cache : /Users/juneyoung/miniconda3/pkgs
/Users/juneyoung/.conda/pkgs
envs directories : /Users/juneyoung/miniconda3/envs
/Users/juneyoung/.conda/envs
platform : osx-64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Darwin/21.4.0 OSX/12.3.1
UID:GID : 501:20
netrc file : None
offline mode : False

(base) [email protected] ~ % conda env create -n qiime2-2022.2 --file qiime2-2022.2-py38-osx-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.

  • failed

I did same way that you recommended!
Conda osx is working on terminal with rosetta model! Thank you!
However, qiime2 is not installed and the conflict issue is still repeated. Hm.. I don't know what is the problem.

@SoilRotifer anaconda works great. I use it all the time, the error I'm getting is the same as Juneyoung.

"Collecting package metadata (repodata.json): done

Solving environment: -

Found conflicts! Looking for incompatible packages.

This can take several minutes. Press CTRL-C to abort."

What I was wondering was if there was any issue using the full anaconda installation as opposed to Miniconda?

Looks like your issues may be resolved over in this thread:

I suggest continuing the dialog over there.

2 Likes

Wow!

Thank you SoilRotifer!!
It was successfully installed and worked well!
I really appreciate you for helping me!

Have a great day!

With intel chip, install regular mini-anaconda or anaconda.
If some issue arises, try the command line " conda env create -n qiime2-2022.2 --file..." some times more.
It will works.

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