Error following installation of qiime2

QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/commands.py", line 77, in get_command
    plugin = self._plugin_lookup[name]
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/commands.py", line 53, in _plugin_lookup
    import q2cli.cache
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 305, in <module>
    CACHE = DeploymentCache()
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 107, in _get_cached_state
    self._cache_current_state(current_requirements)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 200, in _cache_current_state
    state = self._get_current_state()
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 232, in _get_current_state
    import qiime2.sdk
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/__init__.py", line 10, in <module>
    from qiime2.metadata import Metadata, MetadataCategory
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/metadata.py", line 13, in <module>
    import pandas as pd
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/pandas/__init__.py", line 19, in <module>
    "Missing required dependencies {0}".format(missing_dependencies))
ImportError: Missing required dependencies ['numpy']

I am pretty much sure my Anaconda3 is the newest version and all the other dependency packages are all the newest version, I just followed the instruction on Qiime2 to installed it and then source activate the qiime2. but in the end, when I type qiime help, it showed the bug above, Anyone can help me with this or what other informations should I provide. I am using LInux RedHat, 64bit

Hi @Spartanzhao,
Can you try this again, but run:

conda update conda

before running the install command? Then, be sure to double check that you’re running the Linux install command, not the macOS install command.

If you’re still getting an error, please include the commands that you’ve run with the error message in your reply.

Thanks!

1 Like

Thanks for the reply, it still didn’t work.
Here are my commands and output result. I am wondering is that the problem of my environment variable? What should I do then my qiime2 can import the numpy package. The numpy package have already installed.

conda update conda
Fetching package metadata ...............
Solving package specifications: .

Package plan for installation in environment /Mega/bioinfo/PMO/zhaoyue/anaconda3:

The following packages will be UPDATED:

    conda: 4.3.21-py36_0 defaults --> 4.3.22-py36_0 conda-forge

Proceed ([y]/n)? y

conda-4.3.22-p 100% |################################| Time: 0:00:13  39.63 kB/s
[[email protected] /home/zhaoyue]$source activate qiime2-2017.6
(qiime2-2017.6) [[email protected] /home/zhaoyue]$qiime help
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/commands.py", line 77, in get_command
    plugin = self._plugin_lookup[name]
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/commands.py", line 53, in _plugin_lookup
    import q2cli.cache
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 305, in <module>
    CACHE = DeploymentCache()
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 107, in _get_cached_state
    self._cache_current_state(current_requirements)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 200, in _cache_current_state
    state = self._get_current_state()
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 232, in _get_current_state
    import qiime2.sdk
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/__init__.py", line 10, in <module>
    from qiime2.metadata import Metadata, MetadataCategory
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/metadata.py", line 13, in <module>
    import pandas as pd
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/pandas/__init__.py", line 19, in <module>
    "Missing required dependencies {0}".format(missing_dependencies))
ImportError: Missing required dependencies ['numpy']
(qiime2-2017.6) [[email protected] /home/zhaoyue]$source deactivate qiime2-2017.6
[[email protected] /home/zhaoyue]$conda remove qiime2-2017.6
Fetching package metadata ...............
Solving package specifications: .

PackageNotFoundError: No packages named 'qiime2-2017.6' found to remove from environment.

[[email protected] /home/zhaoyue]$source acitvate qiime2-2017.6
-bash: acitvate: No such file or directory
[[email protected] /home/zhaoyue]$source activate qiime2-2017.6
(qiime2-2017.6) [[email protected] /home/zhaoyue]$conda remove qiime2-2017.6
Fetching package metadata ...............
Solving package specifications: .

PackageNotFoundError: No packages named 'qiime2-2017.6' found to remove from environment.

(qiime2-2017.6) [[email protected] /home/zhaoyue]$qiime help
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/commands.py", line 77, in get_command
    plugin = self._plugin_lookup[name]
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/commands.py", line 53, in _plugin_lookup
    import q2cli.cache
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 305, in <module>
    CACHE = DeploymentCache()
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 107, in _get_cached_state
    self._cache_current_state(current_requirements)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 200, in _cache_current_state
    state = self._get_current_state()
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 232, in _get_current_state
    import qiime2.sdk
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/__init__.py", line 10, in <module>
    from qiime2.metadata import Metadata, MetadataCategory
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/metadata.py", line 13, in <module>
    import pandas as pd
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/pandas/__init__.py", line 19, in <module>
    "Missing required dependencies {0}".format(missing_dependencies))
ImportError: Missing required dependencies ['numpy']
(qiime2-2017.6) [[email protected] /home/zhaoyue]$source deactivate qiime2-2017.6
[[email protected] /home/zhaoyue]$rm -r /Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6
^C
[[email protected] /home/zhaoyue]$cd /Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/
[[email protected] /Mega/bioinfo/PMO/zhaoyue/anaconda3/envs]$rm qiime2-2017.6
rm: cannot remove `qiime2-2017.6': Is a directory
[[email protected] /Mega/bioinfo/PMO/zhaoyue/anaconda3/envs]$rm -r qiime2-2017.6
[[email protected] /Mega/bioinfo/PMO/zhaoyue/anaconda3/envs]$cd ../..
[[email protected] /Mega/bioinfo/PMO/zhaoyue]$packet_write_wait: Connection to 172.16.0.50 port 22: Broken pipe
YuedeMacBook-Pro:~ yuezhao$ ssh [email protected]
[email protected]'s password: 
Last login: Mon Jul 24 09:45:35 2017 from 192.168.2.186
[[email protected] /home/zhaoyue]$conda create -n qiime2-2017.6 --file https://data.qiime2.org/distro/core/qiime2-2017.6-conda-linux-64.txt
dbus post-link :: /etc/machine-id not found ..
dbus post-link :: .. using /proc/sys/kernel/random/boot_id

[[email protected] /home/zhaoyue]$source activate qiime2-2017.6
(qiime2-2017.6) [[email protected] /home/zhaoyue]$qiime help
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/commands.py", line 77, in get_command
    plugin = self._plugin_lookup[name]
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/commands.py", line 53, in _plugin_lookup
    import q2cli.cache
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 305, in <module>
    CACHE = DeploymentCache()
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 107, in _get_cached_state
    self._cache_current_state(current_requirements)
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 200, in _cache_current_state
    state = self._get_current_state()
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 232, in _get_current_state
    import qiime2.sdk
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/__init__.py", line 10, in <module>
    from qiime2.metadata import Metadata, MetadataCategory
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/metadata.py", line 13, in <module>
    import pandas as pd
  File "/Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/pandas/__init__.py", line 19, in <module>
    "Missing required dependencies {0}".format(missing_dependencies))
ImportError: Missing required dependencies ['numpy']

The error message from conda is a bit cryptic here, but the hint is that conda thinks you are trying to remove a conda package called qiime2-2017.6, when I suspect you are actually trying to remove a conda environment called qiime2-2017.6:

$ conda env remove -n qiime2-2017.6

After you have removed the environment, you can confirm that it is gone by checking the list of available conda environments:

$ conda env list

Finally, go ahead and follow the linux installation instructions, as suggested by @gregcaporaso above. Let us know how it goes! Thanks!

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