issues with qiime2 install

Technical Support
1

Hi I tried installing based on this link:
https://docs.qiime2.org/2020.2/install/native/

It has an error at this step:
conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-osx-conda.yml

Thank you!

(base) MacBook-Pro:~ user$ conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-osx-conda.yml

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
        return func(*args, **kwargs)
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda_env/cli/main.py", line 80, in do_call
        exit_code = getattr(module, func_name)(args, parser)
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 80, in execute
        directory=os.getcwd())
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda_env/specs/__init__.py", line 40, in detect
        if spec.can_handle():
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda_env/specs/yaml_file.py", line 18, in can_handle
        self._environment = env.from_file(self.filename)
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda_env/env.py", line 151, in from_file
        return from_yaml(yamlstr, filename=filename)
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda_env/env.py", line 136, in from_yaml
        data = yaml_load_standard(yamlstr)
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/conda/common/serialize.py", line 76, in yaml_load_standard
        return yaml.load(string, Loader=yaml.Loader, version="1.2")
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/main.py", line 935, in load
        return loader._constructor.get_single_data()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/constructor.py", line 109, in get_single_data
        node = self.composer.get_single_node()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/composer.py", line 78, in get_single_node
        document = self.compose_document()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/composer.py", line 104, in compose_document
        self.parser.get_event()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/parser.py", line 163, in get_event
        self.current_event = self.state()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/parser.py", line 239, in parse_document_end
        token = self.scanner.peek_token()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/scanner.py", line 182, in peek_token
        self.fetch_more_tokens()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/scanner.py", line 282, in fetch_more_tokens
        return self.fetch_value()
      File "/Users/user/opt/miniconda3/lib/python3.7/site-packages/ruamel_yaml/scanner.py", line 655, in fetch_value
        self.reader.get_mark(),
    ruamel_yaml.scanner.ScannerError: mapping values are not allowed here
      in "<unicode string>", line 4, column 56:
         ... cted automatically to target URL: <a href="https://raw.githubuse ... 
                                             ^ (line: 4)

`$ /Users/user/opt/miniconda3/bin/conda-env create -n qiime2-2020.2 --file qiime2-2020.2-py36-osx-conda.yml`

  environment variables:
                 CIO_TEST=<not set>
  CONDA_AUTO_UPDATE_CONDA=false
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/Users/user/opt/miniconda3/bin/conda
             CONDA_PREFIX=/Users/user/opt/miniconda3
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/Users/user/opt/miniconda3/bin/python
               CONDA_ROOT=/Users/user/opt/miniconda3
              CONDA_SHLVL=1
                     PATH=/Users/user/opt/miniconda3/bin:/Users/user/opt/miniconda3/
                          bin:/Users/user/opt/miniconda3/condabin:/Library/Frameworks/Pyth
                          on.framework/Versions/3.8/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/
                          sbin:/Library/TeX/texbin:/opt/X11/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : base
    active env location : /Users/user/opt/miniconda3
            shell level : 1
       user config file : /Users/user/.condarc
 populated config files : /Users/user/.condarc
          conda version : 4.8.2
    conda-build version : not installed
         python version : 3.7.6.final.0
       virtual packages : __osx=10.14.6
       base environment : /Users/user/opt/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/anaconda/osx-64
                          https://conda.anaconda.org/anaconda/noarch
                          https://conda.anaconda.org/biocore/osx-64
                          https://conda.anaconda.org/biocore/noarch
                          https://conda.anaconda.org/bioconda/osx-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/qiime2/osx-64
                          https://conda.anaconda.org/qiime2/noarch
                          https://conda.anaconda.org/qiime2/label/r2020.2/osx-64
                          https://conda.anaconda.org/qiime2/label/r2020.2/noarch
          package cache : /Users/user/opt/miniconda3/pkgs
                          /Users/user/.conda/pkgs
       envs directories : /Users/user/opt/miniconda3/envs
                          /Users/user/.conda/envs
               platform : osx-64
             user-agent : conda/4.8.2 requests/2.23.0 CPython/3.7.6 Darwin/18.7.0 OSX/10.14.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False
2

Hello Elizabeth,

Welcome to the Qiime 2 forums. :qiime2: Thanks for posting the detailed error message.

I've received errors like this when my qiime2-2020.2-py36-osx-conda.yml was messed up or didn't fully download. Could you post the last few lines of that file just to make sure it looks alright?

tail qiime2-2020.2-py36-osx-conda.yml

Thanks,
Colin

3

This is what the yml file says (tail just prints this):

Redirecting...

Redirecting...

You should be redirected automatically to target URL: https://raw.githubusercontent.com/qiime2/environment-files/master/2020.2/release/qiime2-2020.2-py36-osx-conda.yml. If not click the link.

And points me to this file:
https://raw.githubusercontent.com/qiime2/environment-files/master/2020.2/release/qiime2-2020.2-py36-osx-conda.yml

I also tried just running these commands directly, and I get the same error.

Thanks!

5

Yeah, it looks like that file failed to download…

Do you have wget installed?

You can run the command by itself, just to make sure it’s working. I have it installed and it shows me this:

(base) %> wget
wget: missing URL
Usage: wget [OPTION]... [URL]...

Try `wget --help' for more options.

Colin