qiime2 2020.11: Install QIIME 2 within a conda environment, failed

Susun · January 9, 2021, 9:52am

HI!I want to install qiime2 2020.11 within a conda environment. When I created a conda environment and install the QIIME 2 2020.11 distribution within the environment, an unexpected error occurred.

Can you tell me why this happened?THANKS!

thermokarst · January 9, 2021, 6:36pm

Hi @Susun - sorry to hear that! Can you please copy the complete error message (as well as the commands you are running)? You'll notice in your screenshot, "conda has prepared the above report" - I think that might be the part that actually tells us what happened. Thanks!

:qiime2:

Susun · January 12, 2021, 4:05pm

Thank you very much for answering my question！This is the complete error report:

time conda env create -n qiime2-2020.11 --file qiime2-2020.11-py36-linux-conda.yml

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

Traceback (most recent call last):
  File "/home/ss/miniconda2/lib/python2.7/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/home/ss/miniconda2/lib/python2.7/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/home/ss/miniconda2/lib/python2.7/site-packages/conda_env/cli/main_create.py", line 80, in execute
    directory=os.getcwd())
  File "/home/ss/miniconda2/lib/python2.7/site-packages/conda_env/specs/__init__.py", line 40, in detect
    if spec.can_handle():
  File "/home/ss/miniconda2/lib/python2.7/site-packages/conda_env/specs/yaml_file.py", line 18, in can_handle
    self._environment = env.from_file(self.filename)
  File "/home/ss/miniconda2/lib/python2.7/site-packages/conda_env/env.py", line 151, in from_file
    return from_yaml(yamlstr, filename=filename)
  File "/home/ss/miniconda2/lib/python2.7/site-packages/conda_env/env.py", line 136, in from_yaml
    data = yaml_load_standard(yamlstr)
  File "/home/ss/miniconda2/lib/python2.7/site-packages/conda/common/serialize.py", line 76, in yaml_load_standard
    return yaml.load(string, Loader=yaml.Loader, version="1.2")
  File "/home/ss/miniconda2/lib/python2.7/site-packages/ruamel_yaml/main.py", line 935, in load
    return loader._constructor.get_single_data()
  File "/home/ss/miniconda2/lib/python2.7/site-packages/ruamel_yaml/constructor.py", line 106, in get_single_data
    node = self.composer.get_single_node()
  File "/home/ss/miniconda2/lib/python2.7/site-packages/ruamel_yaml/composer.py", line 78, in get_single_node
    document = self.compose_document()
  File "/home/ss/miniconda2/lib/python2.7/site-packages/ruamel_yaml/composer.py", line 104, in compose_document
    self.parser.get_event()
  File "/home/ss/miniconda2/lib/python2.7/site-packages/ruamel_yaml/parser.py", line 163, in get_event
    self.current_event = self.state()
  File "/home/ss/miniconda2/lib/python2.7/site-packages/ruamel_yaml/parser.py", line 239, in parse_document_end
    token = self.scanner.peek_token()
  File "/home/ss/miniconda2/lib/python2.7/site-packages/ruamel_yaml/scanner.py", line 182, in peek_token
    self.fetch_more_tokens()
  File "/home/ss/miniconda2/lib/python2.7/site-packages/ruamel_yaml/scanner.py", line 321, in fetch_more_tokens
    self.reader.get_mark(),
ScannerError: while scanning for the next token
found character '\t' that cannot start any token
  in "<byte string>", line 13, column 1:
    	location="ac_detect.php?"+"ac_i ... 
    ^ (line: 13)

$ /home/ss/miniconda2/bin/conda-env create -n qiime2-2020.11 --file qiime2-2020.11-py36-linux-conda.yml

environment variables:
CIO_TEST=
CLASSPATH=:/usr/local/java/jdk1.8.0_161/lib/:/usr/local/java/jdk1.8.0_161/lib/
CONDA_AUTO_UPDATE_CONDA=false
CONDA_EXE=/home/ss/miniconda2/bin/conda
CONDA_PYTHON_EXE=/home/ss/miniconda2/bin/python
CONDA_ROOT=/home/ss/miniconda2
CONDA_SHLVL=0
PATH=/home/ss/miniconda2/bin:/home/ss/miniconda2/condabin:/usr/local/sbin
:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/ga
mes:/snap/bin:/home/ss/R
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=

 active environment : None
        shell level : 0
   user config file : /home/ss/.condarc

An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve
future releases of conda.
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$ conda config --set report_errors true

andrewsanchez · January 12, 2021, 10:17pm

Hi Susan,

I wonder if the environment file you downloaded (qiime2-2020.11-py36-linux-conda.yml) has been modified/corrupted. It sounds to me like a tab character snuck into that file. Is it possible that you opened this file and edited it, perhaps by mistake? My first suggestion is to delete that file and re-download it, e.g.:

rm qiime2-2020.11-py36-linux-conda.yml
wget https://data.qiime2.org/distro/core/qiime2-2020.11-py36-linux-conda.yml

Then try running conda env create -n qiime2-2020.11 --file qiime2-2020.11-py36-linux-conda.yml again.

(see instructions for details here).

system · February 14, 2021, 2:05am

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