Qiime2- 2018.11 doesn't work on

Technical Support
1

I followed the instructions of "Natively installing QIIME 2" using the Miniconda on Ubuntu, but “qiime --help” doesn’t work.
see below:

ac@ac-SUPER ~ $ source activate qiime2-2018.11
Traceback (most recent call last):
File "/home/ac/miniconda3/envs/qiime2-2018.11/bin/qiime", line 11, in
sys.exit(qiime())
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 716, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 641, in make_context
self.parse_args(ctx, args)
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 1086, in parse_args
echo(ctx.get_help(), color=ctx.color)
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 516, in get_help
return self.command.get_help(self)
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 879, in get_help
self.format_help(ctx, formatter)
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 898, in format_help
self.format_options(ctx, formatter)
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 1017, in format_options
self.format_commands(ctx, formatter)
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 1061, in format_commands
for subcommand in self.list_commands(ctx):
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py", line 91, in list_commands
plugins = sorted(self._plugin_lookup)
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py", line 75, in _plugin_lookup
import q2cli.cache
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/cache.py", line 301, in
CACHE = DeploymentCache()
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/cache.py", line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/cache.py", line 93, in _get_cached_state
current_requirements = self._get_current_requirements()
File "/home/ac/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/cache.py", line 131, in _get_current_requirements
import pkg_resources
File "/home/ac/software/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 45
def _bypass_ensure_directory(name, mode=0777):
^
SyntaxError: invalid token

2

Looks like some environment-related issues --- notice your command was run in Python 2.7:

Which is why you saw that SyntaxError. Usually these kinds of issue crop up when you have a PYTHONPATH env var set - what does echo $PYTHONPATH say?

3

Hi thermokarst
please see the ERROR REPORT:

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

Traceback (most recent call last):
  File "/home/ac/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 819, in __call__
    return func(*args, **kwargs)
  File "/home/ac/miniconda3/lib/python3.7/site-packages/conda_env/cli/main.py", line 74, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/home/ac/miniconda3/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 108, in execute
    installer.install(prefix, pkg_specs, args, env)
  File "/home/ac/miniconda3/lib/python3.7/site-packages/conda_env/installers/pip.py", line 40, in _pip_install_via_requirements
    args, pip_version = pip_args(prefix)
  File "/home/ac/miniconda3/lib/python3.7/site-packages/conda_env/pip_util.py", line 33, in pip_args
    pip_version = subprocess.check_output(ret + ['-V']).decode('utf-8').split()[1]
  File "/home/ac/miniconda3/lib/python3.7/subprocess.py", line 389, in check_output
    **kwargs).stdout
  File "/home/ac/miniconda3/lib/python3.7/subprocess.py", line 481, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['/home/ac/miniconda3/envs/qiime2-2018.11/bin/python', '/home/ac/miniconda3/envs/qiime2-2018.11/bin/pip', '-V']' returned non-zero exit status 1.

$ /home/ac/miniconda3/bin/conda-env create -n qiime2-2018.11 --file qiime2-2018.11-py35-linux-conda.yml

environment variables:
CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/ac/miniconda3/bin/conda
CONDA_PREFIX=/home/ac/miniconda3
CONDA_PROMPT_MODIFIER=
CONDA_PYTHON_EXE=/home/ac/miniconda3/bin/python
CONDA_ROOT=/home/ac/miniconda3
CONDA_SHLVL=1
DEFAULTS_PATH=/usr/share/gconf/default.default.path
LD_LIBRARY_PATH=/home/ac/software/qiime/qiime_software/python-2.7.3-release/lib
MANDATORY_PATH=/usr/share/gconf/default.mandatory.path
PATH=/home/ac/miniconda3/bin:/home/ac/miniconda2/bin:/home/ac/software/qiim
e/qiime_software/qiime-galaxy-0.0.1-repository-c2814c3c/scripts:/home/
ac/software/qiime/qiime_software/qiime-1.8.0-release/bin:/home/ac/soft
ware/qiime/qiime_software/tax2tree-1.0-release/bin:/home/ac/software/q
iime/qiime_software/biom-format-1.3.1-release/bin:/home/ac/software/qi
ime/qiime_software/pprospector-1.0.1-release/bin:/home/ac/software/qii
me/qiime_software/pynast-1.2.2-release/bin:/home/ac/software/qiime/qii
me_software/emperor-0.9.3-release/bin:/home/ac/software/qiime/qiime_so
ftware/pyqi-0.3.1-release/bin:/home/ac/software/qiime/qiime_software/q
cli-0.1.0-release/bin:/home/ac/software/qiime/qiime_software/ipython-
latest-repository-a1f621bf/bin:/home/ac/software/qiime/qiime_software/
tornado-3.1.1-release/bin:/home/ac/software/qiime/qiime_software/pyzmq
-2.1.11-release/bin:/home/ac/software/qiime/qiime_software/uclust-1.2.
22-release/.:/home/ac/software/qiime/qiime_software/cdhit-3.1-release/
.:/home/ac/software/qiime/qiime_software/r-3.0.2-release/bin:/home/ac/
software/qiime/qiime_software/SeqPrep-latest-repository-85e2389e/.:/ho
me/ac/software/qiime/qiime_software/rdpclassifier-2.2-release/.:/home/
ac/software/qiime/qiime_software/muscle-3.8.31-release/.:/home/ac/soft
ware/qiime/qiime_software/parsinsert-1.0.4-release/.:/home/ac/software
/qiime/qiime_software/blast-2.2.22-release/bin:/home/ac/software/qiime
/qiime_software/pplacer-1.1-release/.:/home/ac/software/qiime/qiime_so
ftware/bwa-0.6.2-release/.:/home/ac/software/qiime/qiime_software/fast
tree-2.1.3-release/.:/home/ac/software/qiime/qiime_software/mothur-1.2
5.0-release/.:/home/ac/software/qiime/qiime_software/ea-utils-1.1.2-53
7-release/.:/home/ac/software/qiime/qiime_software/vienna-1.8.4-releas
e/.:/home/ac/software/qiime/qiime_software/infernal-1.0.2-release/bin:
/home/ac/software/qiime/qiime_software/cdbtools-10.11.2010-release/.:confused:
home/ac/software/qiime/qiime_software/drisee-1.2-release/.:/home/ac/so
ftware/qiime/qiime_software/python-2.7.3-release/bin:/home/ac/software
/qiime/qiime_software/chimeraslayer-4.29.2010-release/ChimeraSlayer:/h
ome/ac/software/qiime/qiime_software/chimeraslayer-4.29.2010-release/N
AST-iEr:/home/ac/software/qiime/qiime_software/cytoscape-2.7.0-release
/.:/home/ac/software/qiime/qiime_software/rtax-0.984-release/.:/home/a
c/software/qiime/qiime_software/sourcetracker-0.9.5-release/.:/home/ac
/software/qiime/qiime_software/blat-34-release/.:/home/ac/software/qii
me/qiime_software/ampliconnoise-1.27-release/Scripts:/home/ac/software
/qiime/qiime_software/ampliconnoise-1.27-release/bin:/home/ac/software
/qiime/qiime_software/raxml-7.3.0-release/.:/home/ac/software/qiime/qi
ime_software/clearcut-1.0.9-release/.:/usr/local/sbin:/usr/local/bin:/
usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
PYTHONPATH=/home/ac/software/qiime/qiime_software/qiime-galaxy-0.0.1-repository-c
2814c3c/lib/:/home/ac/software/qiime/qiime_software/qiime-1.8.0-releas
e/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/t
ax2tree-1.0-release/lib/python2.7/site-
packages:/home/ac/software/qiime/qiime_software/biom-
format-1.3.1-release/lib/python2.7/site-packages:/home/ac/software/qii
me/qiime_software/pynast-1.2.2-release/lib/python2.7/site-packages:/ho
me/ac/software/qiime/qiime_software/pprospector-1.0.1-release/lib/pyth
on2.7/site-packages:/home/ac/software/qiime/qiime_software/qiime-1.8.0
-release/lib/:/home/ac/software/qiime/qiime_software/emperor-0.9.3-rel
ease/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_softwar
e/sphinx-1.0.4-release/lib/python2.7/site-packages:/home/ac/software/q
iime/qiime_software/pyqi-0.3.1-release/lib/python2.7/site-packages:/ho
me/ac/software/qiime/qiime_software/matplotlib-1.3.1-release/lib/pytho
n2.7/site-packages:/home/ac/software/qiime/qiime_software/MySQL-
python-1.2.3-release/lib/python2.7/site-packages:/home/ac/software/qii
me/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages:/
home/ac/software/qiime/qiime_software/mpi4py-1.2.2-release/lib/python2
.7/site-packages:/home/ac/software/qiime/qiime_software/setuptools-0.6
c11-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_
software/pysqlite-2.6.3-release/lib/python2.7/site-packages:/home/ac/s
oftware/qiime/qiime_software/gdata-2.0.17-release/lib/python2.7/site-p
ackages:/home/ac/software/qiime/qiime_software/tornado-3.1.1-release/l
ib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/pyzm
q-2.1.11-release/lib/python2.7/site-packages:/home/ac/software/qiime/q
iime_software/qcli-0.1.0-release/lib/python2.7/site-
packages:/home/ac/software/qiime/qiime_software/ipython-latest-
repository-a1f621bf/lib/python2.7/site-packages:/home/ac/software/qiim
e/qiime_software/pysqlite-2.6.3-release/lib/:/home/ac/software/qiime/q
iime_software/numpy-1.7.1-release/lib/python2.7/site-packages:/home/ac
/software/qiime/qiime_software/SQLAlchemy-0.7.1-release/lib/python2.7/
site-packages:
RDP_JAR_PATH=/home/ac/software/qiime/qiime_software/rdpclassifier-2.2-release/rdp_c
lassifier-2.2.jar
REQUESTS_CA_BUNDLE=
SOURCETRACKER_PATH=/home/ac/software/qiime/qiime_software/sourcetracker-0.9.5-release/.
SSL_CERT_FILE=
WINDOWPATH=8

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

populated config files :
conda version : 4.5.12
conda-build version : not installed
python version : 3.7.1.final.0
base environment : /home/ac/miniconda3 (writable)
channel URLs : main/linux-64
main/noarch
Anaconda packages for Linux x86_64 (64-bit)
Anaconda packages (noarch)
r/linux-64
r/noarch
Anaconda extras for Linux x86_64 (64-bit)
Anaconda extras (noarch)
package cache : /home/ac/miniconda3/pkgs
/home/ac/.conda/pkgs
envs directories : /home/ac/miniconda3/envs
/home/ac/.conda/envs
platform : linux-64
user-agent : conda/4.5.12 requests/2.21.0 CPython/3.7.1 Linux/3.13.0-24-generic ubuntu/14.04 glibc/2.19
UID:GID : 1000:1000
netrc file : None
offline mode : False

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.
Would you like conda to send this report to the core maintainers?

4

ac@ac-SUPER ~/software/qiime2 which conda /home/ac/miniconda2/bin/conda ac@ac-SUPER ~/software/qiime2 conda --version
conda 4.5.12
ac@ac-SUPER ~/software/qiime2 which python /home/ac/miniconda2/bin/python ac@ac-SUPER ~/software/qiime2 python --version
Python 2.7.15 :: Anaconda, Inc.
ac@ac-SUPER ~/software/qiime2 $ echo PATH /home/ac/miniconda3/bin:/home/ac/miniconda2/bin:/home/ac/software/qiime/qiime_software/qiime-galaxy-0.0.1-repository-c2814c3c/scripts:/home/ac/software/qiime/qiime_software/qiime-1.8.0-release/bin:/home/ac/software/qiime/qiime_software/tax2tree-1.0-release/bin:/home/ac/software/qiime/qiime_software/biom-format-1.3.1-release/bin:/home/ac/software/qiime/qiime_software/pprospector-1.0.1-release/bin:/home/ac/software/qiime/qiime_software/pynast-1.2.2-release/bin:/home/ac/software/qiime/qiime_software/emperor-0.9.3-release/bin:/home/ac/software/qiime/qiime_software/pyqi-0.3.1-release/bin:/home/ac/software/qiime/qiime_software/qcli-0.1.0-release/bin:/home/ac/software/qiime/qiime_software/ipython-latest-repository-a1f621bf/bin:/home/ac/software/qiime/qiime_software/tornado-3.1.1-release/bin:/home/ac/software/qiime/qiime_software/pyzmq-2.1.11-release/bin:/home/ac/software/qiime/qiime_software/uclust-1.2.22-release/.:/home/ac/software/qiime/qiime_software/cdhit-3.1-release/.:/home/ac/software/qiime/qiime_software/r-3.0.2-release/bin:/home/ac/software/qiime/qiime_software/SeqPrep-latest-repository-85e2389e/.:/home/ac/software/qiime/qiime_software/rdpclassifier-2.2-release/.:/home/ac/software/qiime/qiime_software/muscle-3.8.31-release/.:/home/ac/software/qiime/qiime_software/parsinsert-1.0.4-release/.:/home/ac/software/qiime/qiime_software/blast-2.2.22-release/bin:/home/ac/software/qiime/qiime_software/pplacer-1.1-release/.:/home/ac/software/qiime/qiime_software/bwa-0.6.2-release/.:/home/ac/software/qiime/qiime_software/fasttree-2.1.3-release/.:/home/ac/software/qiime/qiime_software/mothur-1.25.0-release/.:/home/ac/software/qiime/qiime_software/ea-utils-1.1.2-537-release/.:/home/ac/software/qiime/qiime_software/vienna-1.8.4-release/.:/home/ac/software/qiime/qiime_software/infernal-1.0.2-release/bin:/home/ac/software/qiime/qiime_software/cdbtools-10.11.2010-release/.:/home/ac/software/qiime/qiime_software/drisee-1.2-release/.:/home/ac/software/qiime/qiime_software/python-2.7.3-release/bin:/home/ac/software/qiime/qiime_software/chimeraslayer-4.29.2010-release/ChimeraSlayer:/home/ac/software/qiime/qiime_software/chimeraslayer-4.29.2010-release/NAST-iEr:/home/ac/software/qiime/qiime_software/cytoscape-2.7.0-release/.:/home/ac/software/qiime/qiime_software/rtax-0.984-release/.:/home/ac/software/qiime/qiime_software/sourcetracker-0.9.5-release/.:/home/ac/software/qiime/qiime_software/blat-34-release/.:/home/ac/software/qiime/qiime_software/ampliconnoise-1.27-release/Scripts:/home/ac/software/qiime/qiime_software/ampliconnoise-1.27-release/bin:/home/ac/software/qiime/qiime_software/raxml-7.3.0-release/.:/home/ac/software/qiime/qiime_software/clearcut-1.0.9-release/.:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ac@ac-SUPER ~/software/qiime2 echo $PYTHONPATH
/home/ac/software/qiime/qiime_software/qiime-galaxy-0.0.1-repository-c2814c3c/lib/:/home/ac/software/qiime/qiime_software/qiime-1.8.0-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/tax2tree-1.0-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/biom-format-1.3.1-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/pynast-1.2.2-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/pprospector-1.0.1-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/qiime-1.8.0-release/lib/:/home/ac/software/qiime/qiime_software/emperor-0.9.3-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/pyqi-0.3.1-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/MySQL-python-1.2.3-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/mpi4py-1.2.2-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/setuptools-0.6c11-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/pysqlite-2.6.3-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/gdata-2.0.17-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/tornado-3.1.1-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/pyzmq-2.1.11-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/qcli-0.1.0-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/ipython-latest-repository-a1f621bf/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/pysqlite-2.6.3-release/lib/:/home/ac/software/qiime/qiime_software/numpy-1.7.1-release/lib/python2.7/site-packages:/home/ac/software/qiime/qiime_software/SQLAlchemy-0.7.1-release/lib/python2.7/site-packages:

6

Well, I think that answers the question! Your PYTHONPATH (and PATH) are pretty packed with stuff that is almost certainly going to cause problems here. It looks like you might have an old QIIME 1 env activated here too. I would suggest cleaning up your deployments here --- either way, your PYTHONPATH is going to cause the most headaches here --- you can unset it, but, that will probably cause problems with the other software that set it in the first place.

8

I have another quesiton about installation of QIIME2.

I download the minocoda package (python 3.7; 64bit, linux) and install it successfully (without any error or environment). Then update conda as suggest. install "wget", and download "qiime2-2018.11-py35-linux-conda.yml";
After running the command "conda env create -n qiime2-2018.11 --file qiime2-2018.11-py35-linux-conda.yml", No any information print on the screen.

When run 'source activate qiime2-2018.11' generate an error;
The output of "conda info --envs" show that no qiime enviroment is created.

Could your give a hint?

Background News:

I don't set the $PYTHONPATH and the output of "conda info" as follows:

active environment : base
active env location : /home/minglei/miniconda3
shell level : 1
user config file : /home/minglei/.condarc
populated config files :
conda version : 4.5.12
conda-build version : not installed
python version : 3.7.1.final.0
base environment : /home/minglei/miniconda3 (writable)
channel URLs : main/linux-64
main/noarch
Anaconda packages for Linux x86_64 (64-bit)
Anaconda packages (noarch)
r/linux-64
r/noarch
Anaconda extras for Linux x86_64 (64-bit)
Anaconda extras (noarch)
package cache : /home/minglei/miniconda3/pkgs
/home/minglei/.conda/pkgs
envs directories : /home/minglei/miniconda3/envs
/home/minglei/.conda/envs
platform : linux-64
user-agent : conda/4.5.12 requests/2.21.0 CPython/3.7.1 Linux/4.4.0-141-generic ubuntu/18.04 glibc/2.27
UID:GID : 1005:1005
netrc file : None
offline mode : False

9

@minglei, this sounds like more of the same problem, unfortunately. It sounds like your environment might be impacting this installation. Can you run env again, so that we can see the updated PATH and PYTHONPATH variables?

10

Thanks for your reply.
For now, I have solved the question. The early failure may be relevant with the unstable network.
When I install qiime2 on another server, there's no any error.

Thanks again.