Following the installation instructions I have set up a conda environment and then installed qiime2 there. But further qiime commands then produce the following error:
>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 "/home/grp2009/miniconda3/envs/qiime2-2017.6/bin/qiime", line 6, in <module>
sys.exit(q2cli.__main__.qiime())
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 696, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 621, in make_context
self.parse_args(ctx, args)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1018, in parse_args
rest = Command.parse_args(self, ctx, args)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 880, in parse_args
value, args = param.handle_parse_result(ctx, opts, args)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1404, in handle_parse_result
self.callback, ctx, self, value)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 78, in invoke_param_callback
return callback(ctx, param, value)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 809, in show_help
echo(ctx.get_help(), color=ctx.color)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 496, in get_help
return self.command.get_help(self)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 830, in get_help
self.format_help(ctx, formatter)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 845, in format_help
self.format_options(ctx, formatter)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 956, in format_options
self.format_commands(ctx, formatter)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1000, in format_commands
for subcommand in self.list_commands(ctx):
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/commands.py", line 69, in list_commands
plugins = sorted(self._plugin_lookup)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/commands.py", line 53, in _plugin_lookup
import q2cli.cache
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 305, in <module>
CACHE = DeploymentCache()
File "/home/grp2009/miniconda3/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 "/home/grp2009/miniconda3/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 "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 200, in _cache_current_state
state = self._get_current_state()
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/cache.py", line 238, in _get_current_state
plugin_manager = qiime2.sdk.PluginManager()
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
self._init()
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 58, in _init
plugin = entry_point.load()
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2258, in load
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2264, in resolve
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2_diversity/__init__.py", line 9, in <module>
from ._alpha import (alpha, alpha_phylogenetic, alpha_group_significance,
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2_diversity/_alpha/__init__.py", line 10, in <module>
from ._method import (alpha, alpha_phylogenetic, phylogenetic_metrics,
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2_diversity/_alpha/_method.py", line 11, in <module>
import skbio.diversity
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/skbio/__init__.py", line 13, in <module>
import skbio.io # noqa
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/skbio/io/__init__.py", line 238, in <module>
import_module('skbio.io.format.lsmat')
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/skbio/io/format/lsmat.py", line 77, in <module>
from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/skbio/stats/distance/__init__.py", line 192, in <module>
from ._base import (DissimilarityMatrixError, DistanceMatrixError,
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 12, in <module>
import matplotlib.pyplot as plt
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/matplotlib/pyplot.py", line 115, in <module>
_backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/matplotlib/backends/__init__.py", line 32, in pylab_setup
globals(),locals(),[backend_name],0)
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/matplotlib/backends/backend_qt5agg.py", line 16, in <module>
from .backend_qt5 import QtCore
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/matplotlib/backends/backend_qt5.py", line 26, in <module>
import matplotlib.backends.qt_editor.figureoptions as figureoptions
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/matplotlib/backends/qt_editor/figureoptions.py", line 20, in <module>
import matplotlib.backends.qt_editor.formlayout as formlayout
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/matplotlib/backends/qt_editor/formlayout.py", line 56, in <module>
from matplotlib.backends.qt_compat import QtGui, QtWidgets, QtCore
File "/home/grp2009/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/matplotlib/backends/qt_compat.py", line 128, in <module>
from PyQt5 import QtCore, QtGui, QtWidgets
ImportError: libGL.so.1: cannot open shared object file: No such file or directory
As a minimal error-producing action, if I load up Python and try the following import, I get the same type of error message:
>>> from PyQt5 import QtCore, QtGui, QtWidgets
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: libGL.so.1: cannot open shared object file: No such file or directory
Actually, it’s enough to just import QtGui or QtWidgets. I’m running all of this on CentOS 6.8 Linux. I don’t have apt-get so this answer doesn’t help me, and I’m not working from a Docker image so this one doesn’t either.