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
[zhaoyue@mu01 /home/zhaoyue]$source activate qiime2-2017.6
(qiime2-2017.6) [zhaoyue@mu01 /home/zhaoyue]$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) [zhaoyue@mu01 /home/zhaoyue]$source deactivate qiime2-2017.6
[zhaoyue@mu01 /home/zhaoyue]$conda remove qiime2-2017.6
Fetching package metadata ...............
Solving package specifications: .
PackageNotFoundError: No packages named 'qiime2-2017.6' found to remove from environment.
[zhaoyue@mu01 /home/zhaoyue]$source acitvate qiime2-2017.6
-bash: acitvate: No such file or directory
[zhaoyue@mu01 /home/zhaoyue]$source activate qiime2-2017.6
(qiime2-2017.6) [zhaoyue@mu01 /home/zhaoyue]$conda remove qiime2-2017.6
Fetching package metadata ...............
Solving package specifications: .
PackageNotFoundError: No packages named 'qiime2-2017.6' found to remove from environment.
(qiime2-2017.6) [zhaoyue@mu01 /home/zhaoyue]$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) [zhaoyue@mu01 /home/zhaoyue]$source deactivate qiime2-2017.6
[zhaoyue@mu01 /home/zhaoyue]$rm -r /Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/qiime2-2017.6
^C
[zhaoyue@mu01 /home/zhaoyue]$cd /Mega/bioinfo/PMO/zhaoyue/anaconda3/envs/
[zhaoyue@mu01 /Mega/bioinfo/PMO/zhaoyue/anaconda3/envs]$rm qiime2-2017.6
rm: cannot remove `qiime2-2017.6': Is a directory
[zhaoyue@mu01 /Mega/bioinfo/PMO/zhaoyue/anaconda3/envs]$rm -r qiime2-2017.6
[zhaoyue@mu01 /Mega/bioinfo/PMO/zhaoyue/anaconda3/envs]$cd ../..
[zhaoyue@mu01 /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
[zhaoyue@mu01 /home/zhaoyue]$conda create -n qiime2-2017.6 --file https://data.qiime2.org/distro/core/qiime2-2017.6-conda-linux-64.txt
dbus post-link :: /etc/machine-id not found ..
dbus post-link :: .. using /proc/sys/kernel/random/boot_id
[zhaoyue@mu01 /home/zhaoyue]$source activate qiime2-2017.6
(qiime2-2017.6) [zhaoyue@mu01 /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']