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

[Juneyoung_Lee (Juneyoung)]

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) juneyoung@Juneyoungui-MacBookAir ~ % 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) juneyoung@Juneyoungui-MacBookAir ~ %

• My conda info is this.
  (base) juneyoung@Juneyoungui-MacBookAir ~ % 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
  bioconda/osx-arm64
  bioconda/noarch
  main/osx-arm64
  main/noarch
  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?

[Juneyoung_Lee (Juneyoung)]

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

(base) juneyoung@Juneyoungui-MacBookAir ~ % 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.

[SoilRotifer (Mike Robeson)]

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

[jconoranderson86 (Conor Anderson)]

@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?

[SoilRotifer (Mike Robeson)]

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.

[Juneyoung_Lee (Juneyoung)]

(base) juneyoung@Juneyoungui-MacBookAir ~ % 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) juneyoung@Juneyoungui-MacBookAir ~ % 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.

[jconoranderson86 (Conor Anderson)]

@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?

[SoilRotifer (Mike Robeson)]

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

Conflicts found when installing qiime2-2022.2 on MacOS 12.2.1

Getting error Found conflicts! Looking for incompatible packages. when trying to install QIIME2 2022.2 on MacOS 12.2.1. I see in forum posts (https://forum.qiime2.org/t/instalation-qiime-2020-11-found-conflicts-looking-for-incompatible-packages/17757) that for previous versions this has been addressed by the development team rebuilding the environment files: " Hey there @PatoUru & @cdiener - @ebolyen did some sleuthing and uncovered some package shuffling related to the r-base package - this a…

I suggest continuing the dialog over there.

[Juneyoung_Lee (Juneyoung)]

Wow!

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

Have a great day!

[rogasan (Winnie Wang)]

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.