Error while installing QIIME2 natively

User Support
1

I followed the instructions to install QIIME2 natively for Linux 64 (64-bit). Also, I make sure to have install the up to data conda version to possibly avoid this. However, I'm getting the following error during the installation test. I'd appreciate to any lead to overcome this. Thank you!

(qiime2-2017.8) william@genobacter:~$ qiime --help
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
Traceback (most recent call last):
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 696, in main
    with self.make_context(prog_name, args, **extra) as ctx:
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 621, in make_context
    self.parse_args(ctx, args)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 1018, in parse_args
    rest = Command.parse_args(self, ctx, args)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 880, in parse_args
    value, args = param.handle_parse_result(ctx, opts, args)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 1404, in handle_parse_result
    self.callback, ctx, self, value)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 78, in invoke_param_callback
    return callback(ctx, param, value)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 809, in show_help
    echo(ctx.get_help(), color=ctx.color)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 496, in get_help
    return self.command.get_help(self)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 830, in get_help
    self.format_help(ctx, formatter)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 845, in format_help
    self.format_options(ctx, formatter)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 956, in format_options
    self.format_commands(ctx, formatter)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 1000, in format_commands
    for subcommand in self.list_commands(ctx):
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/commands.py", line 69, in list_commands
    plugins = sorted(self._plugin_lookup)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/commands.py", line 53, in _plugin_lookup
    import q2cli.cache
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 306, in <module>
    CACHE = DeploymentCache()
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 107, in _get_cached_state
    self._cache_current_state(current_requirements)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 200, in _cache_current_state
    state = self._get_current_state()
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 238, in _get_current_state
    plugin_manager = qiime2.sdk.PluginManager()
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
    self._init()
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 58, in _init
    plugin = entry_point.load()
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2258, in load
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2264, in resolve
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_gneiss/plugin_setup.py", line 32, in <module>
    importlib.import_module('q2_gneiss.composition')
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_gneiss/composition/__init__.py", line 8, in <module>
    from ._composition import ilr_transform
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_gneiss/composition/_composition.py", line 8, in <module>
    from q2_types.tree import Hierarchy
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_types/__init__.py", line 18, in <module>
    importlib.import_module('q2_types.feature_data')
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_types/feature_data/__init__.py", line 11, in <module>
    from ._format import (
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_types/feature_data/_format.py", line 9, in <module>
    import skbio.io
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/skbio/__init__.py", line 13, in <module>
    import skbio.io  # noqa
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/skbio/io/__init__.py", line 238, in <module>
    import_module('skbio.io.format.lsmat')
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/skbio/io/format/lsmat.py", line 77, in <module>
    from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/skbio/stats/distance/__init__.py", line 192, in <module>
    from ._base import (DissimilarityMatrixError, DistanceMatrixError,
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 12, in <module>
    import matplotlib.pyplot as plt
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/matplotlib/pyplot.py", line 29, in <module>
    import matplotlib.colorbar
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/matplotlib/colorbar.py", line 32, in <module>
    import matplotlib.artist as martist
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/matplotlib/artist.py", line 15, in <module>
    from .transforms import (Bbox, IdentityTransform, TransformedBbox,
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/matplotlib/transforms.py", line 39, in <module>
    from matplotlib._path import (affine_transform, count_bboxes_overlapping_bbox,
ImportError: numpy.core.multiarray failed to import

My Linux distro is Ubuntu (64-bit system). More information below.

(qiime2-2017.8) william@genobacter:~$ conda --version
conda 4.3.25
(qiime2-2017.8) william@genobacter:~$ which conda
/home/william/Programs/miniconda2/envs/qiime2-2017.8/bin/conda
(qiime2-2017.8) william@genobacter:~$ which python
/home/william/Programs/miniconda2/envs/qiime2-2017.8/bin/python
(qiime2-2017.8) william@genobacter:~$ python --version
Python 3.5.4 :: Continuum Analytics, Inc.
(qiime2-2017.8) william@genobacter:~$ conda list
# packages in environment at /home/william/Programs/miniconda2/envs/qiime2-2017.8:
#
bioconductor-biobase      2.34.0                 r3.3.1_0    bioconda
bioconductor-biocgenerics 0.20.0                 r3.3.1_0    bioconda
bioconductor-biocparallel 1.6.6                  r3.3.1_0    bioconda
bioconductor-biostrings   2.42.1                 r3.3.1_0    bioconda
bioconductor-dada2        1.4.0                  r3.3.1_0    bioconda
bioconductor-genomeinfodb 1.10.3                 r3.3.1_0    bioconda
bioconductor-genomicalignments 1.8.4                  r3.3.1_0    bioconda
bioconductor-genomicranges 1.26.4                 r3.3.1_0    bioconda
bioconductor-iranges      2.8.2                  r3.3.1_0    bioconda
bioconductor-rsamtools    1.24.0                 r3.3.1_0    bioconda
bioconductor-s4vectors    0.12.2                 r3.3.1_0    bioconda
bioconductor-shortread    1.32.0                 r3.3.1_0    bioconda
bioconductor-summarizedexperiment 1.2.3                  r3.3.1_0    bioconda
bioconductor-xvector      0.14.1                 r3.3.1_0    bioconda
bioconductor-zlibbioc     1.20.0                 r3.3.1_0    bioconda
biom-format               2.1.5                    py35_3    qiime2
bkcharts                  0.2                      py35_0  
blast                     2.6.0               boost1.61_1    bioconda
bleach                    1.5.0                    py35_0  
bokeh                     0.12.7                   py35_0  
boost                     1.61.0                   py35_0  
bzip2                     1.0.6                         3  
cachecontrol              0.12.3                   py35_0  
cairo                     1.14.8                        0  
click                     6.7                      py35_0  
curl                      7.54.1                        0  
cycler                    0.10.0                   py35_0  
dbus                      1.10.20                       0  
deblur                    1.0.2                    py35_0    biocore
decorator                 4.1.2                    py35_0  
emperor                   1.0.0beta8               py35_2    conda-forge
entrypoints               0.2.3                    py35_0  
expat                     2.1.0                         0  
fastcluster               1.1.23              np113py35_0    conda-forge
fasttree                  2.1.9                         2    bioconda
fontconfig                2.12.1                        3  
freetype                  2.5.5                         2  
future                    0.16.0                   py35_1  
glib                      2.50.2                        1  
gneiss                    0.4.1            py35h6d0efef_6    biocore
gsl                       2.2.1                         0  
gst-plugins-base          1.8.0                         0  
gstreamer                 1.8.0                         0  
h5py                      2.7.0               np113py35_0  
harfbuzz                  0.9.39                        2  
hdf5                      1.8.17                        2  
html5lib                  0.9999999                py35_0  
icu                       54.1                          0  
ijson                     2.3                      py35_0    qiime2
ipykernel                 4.6.1                    py35_0  
ipython                   6.1.0                    py35_0  
ipython_genutils          0.2.0                    py35_0  
ipywidgets                6.0.0                    py35_0  
jbig                      2.1                           0  
jedi                      0.10.2                   py35_2  
jinja2                    2.9.6                    py35_0  
jpeg                      9b                            0  
jsonschema                2.6.0                    py35_0  
jupyter_client            5.1.0                    py35_0  
jupyter_core              4.3.0                    py35_0  
krb5                      1.13.2                        0  
libffi                    3.2.1                         1  
libgcc                    5.2.0                         0  
libgfortran               3.0.0                         1  
libiconv                  1.14                          0  
libpng                    1.6.30                        1  
libsodium                 1.0.10                        0  
libssh2                   1.8.0                         0  
libtiff                   4.0.6                         3  
libxcb                    1.12                          1  
libxml2                   2.9.4                         0  
lockfile                  0.12.2                   py35_0  
mafft                     7.221                         0    bioconda
markupsafe                1.0                      py35_0  
matplotlib                2.0.2               np113py35_0  
mistune                   0.7.4                    py35_0  
mkl                       2017.0.3                      0  
msgpack-python            0.4.8                    py35_0  
natsort                   5.1.0                    py35_0  
nbconvert                 5.2.1                    py35_0  
nbformat                  4.4.0                    py35_0  
ncurses                   5.9                          10  
nose                      1.3.7                    py35_1  
notebook                  5.0.0                    py35_0  
numpy                     1.13.1                   py35_0  
openssl                   1.0.2l                        0  
pandas                    0.20.3                   py35_0  
pandocfilters             1.4.2                    py35_0  
pango                     1.40.3                        1  
path.py                   10.3.1                   py35_0  
patsy                     0.4.1                    py35_0  
pcre                      8.39                          1  
pexpect                   4.2.1                    py35_0  
pickleshare               0.7.4                    py35_0  
pip                       9.0.1                    py35_1  
pixman                    0.34.0                        0  
prompt_toolkit            1.0.15                   py35_0  
psutil                    5.2.2                    py35_0  
ptyprocess                0.5.2                    py35_0  
pygments                  2.2.0                    py35_0  
pyparsing                 2.2.0                    py35_0  
pyqt                      5.6.0                    py35_2  
python                    3.5.4                         0  
python-dateutil           2.6.1                    py35_0  
pytz                      2017.2                   py35_0  
pyyaml                    3.12                     py35_0  
pyzmq                     16.0.2                   py35_0  
q2-alignment              2017.8.0                 py35_0    qiime2/label/r2017.8
q2-composition            2017.8.0                 py35_0    qiime2/label/r2017.8
q2-dada2                  2017.8.0                 py35_0    qiime2/label/r2017.8
q2-deblur                 2017.8.0                 py35_0    qiime2/label/r2017.8
q2-demux                  2017.8.0                 py35_0    qiime2/label/r2017.8
q2-diversity              2017.8.0                 py35_0    qiime2/label/r2017.8
q2-emperor                2017.8.0                 py35_0    qiime2/label/r2017.8
q2-feature-classifier     2017.8.0                 py35_0    qiime2/label/r2017.8
q2-feature-table          2017.8.0                 py35_0    qiime2/label/r2017.8
q2-gneiss                 2017.8.0                 py35_0    qiime2/label/r2017.8
q2-longitudinal           2017.8.0                 py35_0    qiime2/label/r2017.8
q2-metadata               2017.8.0                 py35_0    qiime2/label/r2017.8
q2-phylogeny              2017.8.0                 py35_0    qiime2/label/r2017.8
q2-quality-filter         2017.8.0                 py35_0    qiime2/label/r2017.8
q2-sample-classifier      2017.8.0                 py35_0    qiime2/label/r2017.8
q2-taxa                   2017.8.0                 py35_0    qiime2/label/r2017.8
q2-types                  2017.8.0                 py35_0    qiime2/label/r2017.8
q2cli                     2017.8.0                 py35_0    qiime2/label/r2017.8
q2templates               2017.8.0                 py35_0    qiime2/label/r2017.8
qiime2                    2017.8.0                 py35_0    qiime2/label/r2017.8
qt                        5.6.2                         5  
r                         3.3.1                  r3.3.1_1  
r-assertthat              0.1                    r3.3.1_4  
r-base                    3.3.1                         6  
r-bh                      1.62.0_1               r3.3.1_0  
r-bitops                  1.0_6                  r3.3.1_2  
r-boot                    1.3_18                 r3.3.1_0  
r-class                   7.3_14                 r3.3.1_0  
r-cluster                 2.0.5                  r3.3.1_0  
r-codetools               0.2_15                 r3.3.1_0  
r-colorspace              1.3_1                  r3.3.1_0  
r-data.table              1.10.0                 r3.3.1_0  
r-dichromat               2.0_0                  r3.3.1_2  
r-digest                  0.6.10                 r3.3.1_0  
r-foreign                 0.8_67                 r3.3.1_0  
r-futile.logger           1.4.1                  r3.3.1_0    bioconda
r-futile.options          1.0.0                  r3.3.1_0    bioconda
r-ggplot2                 2.2.0                  r3.3.1_0  
r-gtable                  0.2.0                  r3.3.1_0  
r-hwriter                 1.3.2                  r3.3.1_0    bioconda
r-kernsmooth              2.23_15                r3.3.1_0  
r-labeling                0.3                    r3.3.1_2  
r-lambda.r                1.1.7                  r3.3.1_0    bioconda
r-lattice                 0.20_34                r3.3.1_0  
r-latticeextra            0.6_28                 r3.3.1_0  
r-lazyeval                0.2.0                  r3.3.1_0  
r-magrittr                1.5                    r3.3.1_2  
r-mass                    7.3_45                 r3.3.1_0  
r-matrix                  1.2_7.1                r3.3.1_0  
r-mgcv                    1.8_12                 r3.3.1_0  
r-munsell                 0.4.3                  r3.3.1_0  
r-nlme                    3.1_128                r3.3.1_0  
r-nnet                    7.3_12                 r3.3.1_0  
r-plyr                    1.8.4                  r3.3.1_0  
r-rcolorbrewer            1.1_2                  r3.3.1_3  
r-rcpp                    0.12.8                 r3.3.1_0  
r-rcppparallel            4.3.20                 r3.3.1_1    bioconda
r-rcurl                   1.95_4.8               r3.3.1_0  
r-recommended             3.3.1                  r3.3.1_0  
r-reshape2                1.4.2                  r3.3.1_0  
r-rpart                   4.1_10                 r3.3.1_0  
r-scales                  0.4.1                  r3.3.1_0  
r-snow                    0.4_1                  r3.3.1_0    bioconda
r-spatial                 7.3_11                 r3.3.1_0  
r-stringi                 1.1.2                  r3.3.1_0  
r-stringr                 1.1.0                  r3.3.1_0  
r-survival                2.39_4                 r3.3.1_0  
r-tibble                  1.2                    r3.3.1_0  
readline                  6.2                           2  
requests                  2.14.2                   py35_0  
scikit-bio                0.5.1               np113py35_0  
scikit-learn              0.19.0              np113py35_0  
scipy                     0.19.1              np113py35_0  
seaborn                   0.8                      py35_0  
setuptools                27.2.0                   py35_0  
simplegeneric             0.8.1                    py35_1  
sip                       4.18                     py35_0  
six                       1.10.0                   py35_0  
sortmerna                 2.0                           1    bioconda
sqlite                    3.13.0                        0  
statsmodels               0.8.0               np113py35_0  
terminado                 0.6                      py35_0  
testpath                  0.3.1                    py35_0  
tk                        8.5.18                        0  
tornado                   4.5.2                    py35_0  
traitlets                 4.3.2                    py35_0  
tzlocal                   1.3                      py35_0    qiime2
vsearch                   2.0.3                         0    bioconda
wcwidth                   0.1.7                    py35_0  
wheel                     0.29.0                   py35_0  
widgetsnbextension        3.0.2                    py35_0  
xz                        5.2.3                         0  
yaml                      0.1.6                         0  
zeromq                    4.1.5                         0  
zlib                      1.2.11                        0
2

Thanks for the very detailed post @wrodriguez!

I'm afraid we haven't seen this before. I'm not able to reproduce either (after updating my conda to match). It almost seems like matplotlib is broken, but every package is exactly pinned in the install file, so nothing should have changed. Your version of numpy look fine (thanks for the conda list!), so I really have no idea what's going on yet.

This is a complete shot in the dark, but does running this in your qiime2-2017.8 environment fix anything?

conda install nomkl
3

Thanks @ebolyen for the suggestion. The nomkl was successfully installed, which also installed openbias (0.2.19-0) and updated numpy, scikit-learn, and scipy. Now, qiime test still not working but the error is different.

(qiime2-2017.8) william@genobacter:~$ 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/william/Programs/miniconda2/envs/qiime2-2017.8/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 696, in main
    with self.make_context(prog_name, args, **extra) as ctx:
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 621, in make_context
    self.parse_args(ctx, args)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 1018, in parse_args
    rest = Command.parse_args(self, ctx, args)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 880, in parse_args
    value, args = param.handle_parse_result(ctx, opts, args)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 1404, in handle_parse_result
    self.callback, ctx, self, value)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 78, in invoke_param_callback
    return callback(ctx, param, value)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 809, in show_help
    echo(ctx.get_help(), color=ctx.color)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 496, in get_help
    return self.command.get_help(self)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 830, in get_help
    self.format_help(ctx, formatter)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 845, in format_help
    self.format_options(ctx, formatter)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 956, in format_options
    self.format_commands(ctx, formatter)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 1000, in format_commands
    for subcommand in self.list_commands(ctx):
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/commands.py", line 69, in list_commands
    plugins = sorted(self._plugin_lookup)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/commands.py", line 53, in _plugin_lookup
    import q2cli.cache
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 306, in <module>
    CACHE = DeploymentCache()
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 107, in _get_cached_state
    self._cache_current_state(current_requirements)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 200, in _cache_current_state
    state = self._get_current_state()
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 238, in _get_current_state
    plugin_manager = qiime2.sdk.PluginManager()
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
    self._init()
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 58, in _init
    plugin = entry_point.load()
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2258, in load
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2264, in resolve
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_feature_classifier/__init__.py", line 15, in <module>
    importlib.import_module('q2_feature_classifier.classifier')
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py", line 251, in <module>
    _register_fitter(name, pipeline)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py", line 215, in _register_fitter
    parameters, signature_params = _pipeline_signature(spec)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py", line 194, in _pipeline_signature
    pipeline = pipeline_from_spec(spec)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py", line 86, in pipeline_from_spec
    steps = json.loads(json.dumps(spec), object_hook=as_steps)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/json/__init__.py", line 332, in loads
    return cls(**kw).decode(s)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
  File "/home/william/Programs/miniconda2/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py", line 83, in as_steps
    return klass(**{k: v for k, v in obj.items() if k != '__type__'})
TypeError: __init__() got an unexpected keyword argument 'alternate_sign'

Here are the packages list just in case.

(qiime2-2017.8) william@genobacter:~$ conda list
# packages in environment at /home/william/Programs/miniconda2/envs/qiime2-2017.8:
#
bioconductor-biobase      2.34.0                 r3.3.1_0    bioconda
bioconductor-biocgenerics 0.20.0                 r3.3.1_0    bioconda
bioconductor-biocparallel 1.6.6                  r3.3.1_0    bioconda
bioconductor-biostrings   2.42.1                 r3.3.1_0    bioconda
bioconductor-dada2        1.4.0                  r3.3.1_0    bioconda
bioconductor-genomeinfodb 1.10.3                 r3.3.1_0    bioconda
bioconductor-genomicalignments 1.8.4                  r3.3.1_0    bioconda
bioconductor-genomicranges 1.26.4                 r3.3.1_0    bioconda
bioconductor-iranges      2.8.2                  r3.3.1_0    bioconda
bioconductor-rsamtools    1.24.0                 r3.3.1_0    bioconda
bioconductor-s4vectors    0.12.2                 r3.3.1_0    bioconda
bioconductor-shortread    1.32.0                 r3.3.1_0    bioconda
bioconductor-summarizedexperiment 1.2.3                  r3.3.1_0    bioconda
bioconductor-xvector      0.14.1                 r3.3.1_0    bioconda
bioconductor-zlibbioc     1.20.0                 r3.3.1_0    bioconda
biom-format               2.1.5                    py35_3    qiime2
bkcharts                  0.2                      py35_0  
blast                     2.6.0               boost1.61_1    bioconda
bleach                    1.5.0                    py35_0  
bokeh                     0.12.7                   py35_0  
boost                     1.61.0                   py35_0  
bzip2                     1.0.6                         3  
cachecontrol              0.12.3                   py35_0  
cairo                     1.14.8                        0  
click                     6.7                      py35_0  
curl                      7.54.1                        0  
cycler                    0.10.0                   py35_0  
dbus                      1.10.20                       0  
deblur                    1.0.2                    py35_0    biocore
decorator                 4.1.2                    py35_0  
emperor                   1.0.0beta8               py35_2    conda-forge
entrypoints               0.2.3                    py35_0  
expat                     2.1.0                         0  
fastcluster               1.1.23              np113py35_0    conda-forge
fasttree                  2.1.9                         2    bioconda
fontconfig                2.12.1                        3  
freetype                  2.5.5                         2  
future                    0.16.0                   py35_1  
glib                      2.50.2                        1  
gneiss                    0.4.1            py35h6d0efef_6    biocore
gsl                       2.2.1                         0  
gst-plugins-base          1.8.0                         0  
gstreamer                 1.8.0                         0  
h5py                      2.7.0               np113py35_0  
harfbuzz                  0.9.39                        2  
hdf5                      1.8.17                        2  
html5lib                  0.9999999                py35_0  
icu                       54.1                          0  
ijson                     2.3                      py35_0    qiime2
ipykernel                 4.6.1                    py35_0  
ipython                   6.1.0                    py35_0  
ipython_genutils          0.2.0                    py35_0  
ipywidgets                6.0.0                    py35_0  
jbig                      2.1                           0  
jedi                      0.10.2                   py35_2  
jinja2                    2.9.6                    py35_0  
jpeg                      9b                            0  
jsonschema                2.6.0                    py35_0  
jupyter_client            5.1.0                    py35_0  
jupyter_core              4.3.0                    py35_0  
krb5                      1.13.2                        0  
libffi                    3.2.1                         1  
libgcc                    5.2.0                         0  
libgfortran               3.0.0                         1  
libiconv                  1.14                          0  
libpng                    1.6.30                        1  
libsodium                 1.0.10                        0  
libssh2                   1.8.0                         0  
libtiff                   4.0.6                         3  
libxcb                    1.12                          1  
libxml2                   2.9.4                         0  
lockfile                  0.12.2                   py35_0  
mafft                     7.221                         0    bioconda
markupsafe                1.0                      py35_0  
matplotlib                2.0.2               np113py35_0  
mistune                   0.7.4                    py35_0  
mkl                       2017.0.3                      0  
msgpack-python            0.4.8                    py35_0  
natsort                   5.1.0                    py35_0  
nbconvert                 5.2.1                    py35_0  
nbformat                  4.4.0                    py35_0  
ncurses                   5.9                          10  
nomkl                     1.0                           0  
nose                      1.3.7                    py35_1  
notebook                  5.0.0                    py35_0  
numpy                     1.13.1             py35_nomkl_0  [nomkl]
openblas                  0.2.19                        0  
openssl                   1.0.2l                        0  
pandas                    0.20.3                   py35_0  
pandocfilters             1.4.2                    py35_0  
pango                     1.40.3                        1  
path.py                   10.3.1                   py35_0  
patsy                     0.4.1                    py35_0  
pcre                      8.39                          1  
pexpect                   4.2.1                    py35_0  
pickleshare               0.7.4                    py35_0  
pip                       9.0.1                    py35_1  
pixman                    0.34.0                        0  
prompt_toolkit            1.0.15                   py35_0  
psutil                    5.2.2                    py35_0  
ptyprocess                0.5.2                    py35_0  
pygments                  2.2.0                    py35_0  
pyparsing                 2.2.0                    py35_0  
pyqt                      5.6.0                    py35_2  
python                    3.5.4                         0  
python-dateutil           2.6.1                    py35_0  
pytz                      2017.2                   py35_0  
pyyaml                    3.12                     py35_0  
pyzmq                     16.0.2                   py35_0  
q2-alignment              2017.8.0                 py35_0    qiime2/label/r2017.8
q2-composition            2017.8.0                 py35_0    qiime2/label/r2017.8
q2-dada2                  2017.8.0                 py35_0    qiime2/label/r2017.8
q2-deblur                 2017.8.0                 py35_0    qiime2/label/r2017.8
q2-demux                  2017.8.0                 py35_0    qiime2/label/r2017.8
q2-diversity              2017.8.0                 py35_0    qiime2/label/r2017.8
q2-emperor                2017.8.0                 py35_0    qiime2/label/r2017.8
q2-feature-classifier     2017.8.0                 py35_0    qiime2/label/r2017.8
q2-feature-table          2017.8.0                 py35_0    qiime2/label/r2017.8
q2-gneiss                 2017.8.0                 py35_0    qiime2/label/r2017.8
q2-longitudinal           2017.8.0                 py35_0    qiime2/label/r2017.8
q2-metadata               2017.8.0                 py35_0    qiime2/label/r2017.8
q2-phylogeny              2017.8.0                 py35_0    qiime2/label/r2017.8
q2-quality-filter         2017.8.0                 py35_0    qiime2/label/r2017.8
q2-sample-classifier      2017.8.0                 py35_0    qiime2/label/r2017.8
q2-taxa                   2017.8.0                 py35_0    qiime2/label/r2017.8
q2-types                  2017.8.0                 py35_0    qiime2/label/r2017.8
q2cli                     2017.8.0                 py35_0    qiime2/label/r2017.8
q2templates               2017.8.0                 py35_0    qiime2/label/r2017.8
qiime2                    2017.8.0                 py35_0    qiime2/label/r2017.8
qt                        5.6.2                         5  
r                         3.3.1                  r3.3.1_1  
r-assertthat              0.1                    r3.3.1_4  
r-base                    3.3.1                         6  
r-bh                      1.62.0_1               r3.3.1_0  
r-bitops                  1.0_6                  r3.3.1_2  
r-boot                    1.3_18                 r3.3.1_0  
r-class                   7.3_14                 r3.3.1_0  
r-cluster                 2.0.5                  r3.3.1_0  
r-codetools               0.2_15                 r3.3.1_0  
r-colorspace              1.3_1                  r3.3.1_0  
r-data.table              1.10.0                 r3.3.1_0  
r-dichromat               2.0_0                  r3.3.1_2  
r-digest                  0.6.10                 r3.3.1_0  
r-foreign                 0.8_67                 r3.3.1_0  
r-futile.logger           1.4.1                  r3.3.1_0    bioconda
r-futile.options          1.0.0                  r3.3.1_0    bioconda
r-ggplot2                 2.2.0                  r3.3.1_0  
r-gtable                  0.2.0                  r3.3.1_0  
r-hwriter                 1.3.2                  r3.3.1_0    bioconda
r-kernsmooth              2.23_15                r3.3.1_0  
r-labeling                0.3                    r3.3.1_2  
r-lambda.r                1.1.7                  r3.3.1_0    bioconda
r-lattice                 0.20_34                r3.3.1_0  
r-latticeextra            0.6_28                 r3.3.1_0  
r-lazyeval                0.2.0                  r3.3.1_0  
r-magrittr                1.5                    r3.3.1_2  
r-mass                    7.3_45                 r3.3.1_0  
r-matrix                  1.2_7.1                r3.3.1_0  
r-mgcv                    1.8_12                 r3.3.1_0  
r-munsell                 0.4.3                  r3.3.1_0  
r-nlme                    3.1_128                r3.3.1_0  
r-nnet                    7.3_12                 r3.3.1_0  
r-plyr                    1.8.4                  r3.3.1_0  
r-rcolorbrewer            1.1_2                  r3.3.1_3  
r-rcpp                    0.12.8                 r3.3.1_0  
r-rcppparallel            4.3.20                 r3.3.1_1    bioconda
r-rcurl                   1.95_4.8               r3.3.1_0  
r-recommended             3.3.1                  r3.3.1_0  
r-reshape2                1.4.2                  r3.3.1_0  
r-rpart                   4.1_10                 r3.3.1_0  
r-scales                  0.4.1                  r3.3.1_0  
r-snow                    0.4_1                  r3.3.1_0    bioconda
r-spatial                 7.3_11                 r3.3.1_0  
r-stringi                 1.1.2                  r3.3.1_0  
r-stringr                 1.1.0                  r3.3.1_0  
r-survival                2.39_4                 r3.3.1_0  
r-tibble                  1.2                    r3.3.1_0  
readline                  6.2                           2  
requests                  2.14.2                   py35_0  
scikit-bio                0.5.1               np113py35_0  
scikit-learn              0.19.0          np113py35_nomkl_0  [nomkl]
scipy                     0.19.1          np113py35_nomkl_0  [nomkl]
seaborn                   0.8                      py35_0  
setuptools                27.2.0                   py35_0  
simplegeneric             0.8.1                    py35_1  
sip                       4.18                     py35_0  
six                       1.10.0                   py35_0  
sortmerna                 2.0                           1    bioconda
sqlite                    3.13.0                        0  
statsmodels               0.8.0               np113py35_0  
terminado                 0.6                      py35_0  
testpath                  0.3.1                    py35_0  
tk                        8.5.18                        0  
tornado                   4.5.2                    py35_0  
traitlets                 4.3.2                    py35_0  
tzlocal                   1.3                      py35_0    qiime2
vsearch                   2.0.3                         0    bioconda
wcwidth                   0.1.7                    py35_0  
wheel                     0.29.0                   py35_0  
widgetsnbextension        3.0.2                    py35_0  
xz                        5.2.3                         0  
yaml                      0.1.6                         0  
zeromq                    4.1.5                         0  
zlib                      1.2.11                        0
4

Well that only makes things strange. I was able to do the same to my environment and do not see the same exception at all (I'm using Arch Linux, but it should be the same to conda). Worse, it looks like numpy is no longer having any issues, but the scikit-learn Python API has changed underfoot.

I'm going to diff my conda environment to yours to see if there's anything obvious, but until then you might try the following:

conda env remove -n qiime2-2017.8  # will delete your existing environment
conda clean --all  # gets rid of all of conda's caching, it can be pretty bad at it
conda create -n qiime2-2017.8 --file https://data.qiime2.org/distro/core/qiime2-2017.8-conda-linux-64.txt

It might not do anything to fix the problem, but stranger things have happened.

5

Followup:

vimdiff doesn't see anything different between my conda list and yours after installing nomkl, so I have no idea why you're getting that exception. I'm really hoping there's something wrong with conda's cache and the conda clean --all fixes things.

6

Unfortunately, no luck. I tried a fresh start as suggested. Also, I installed Miniconda3 after removed completely Miniconda2, but the same error showed up. This after also running conda install nomkl. Would you recommend to try something else?

I really appreciate all your help and time trying to figure out this issue.

-- Will

8

That's a bummer!

Just for completeness' sake, do you get the two errors in their corresponding situations with Miniconda3 (i.e. exactly the same as the above posts)?

Do you by chance have any PYTHONPATH variables set in your environment? Also, if you don't have an environment activated, does the following fail with a ModuleNotFound error? (it should)

python -c "import numpy"
python -c "import scipy"

Something else that has just occurred to me is that conda list makes some (reasonable) assumptions as to how packages are loaded which is not entirely the same as Python's. So in strange situations, it's possible for a different package to be loaded at runtime altogether. To my knowledge, pip has a more complete notion of what Python will load at any given time.

What does this command say in your environment (let me know if nomkl is in there also)?

pip freeze

Finally, last shot in the dark is, what do these commands say:

lscpu
uname --all

Are you running a virtual machine of any kind, or is this OS on bare metal so to speak?

Thanks, hopefully one of these ideas will turn up something!

10

Yes, @ebolyen. I am getting the same problem with Miniconda2 and Miniconda3 (see below).

(qiime2-2017.8) william@genobacter:~$ 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/william/miniconda3/envs/qiime2-2017.8/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 696, in main
    with self.make_context(prog_name, args, **extra) as ctx:
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 621, in make_context
    self.parse_args(ctx, args)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 1018, in parse_args
    rest = Command.parse_args(self, ctx, args)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 880, in parse_args
    value, args = param.handle_parse_result(ctx, opts, args)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 1404, in handle_parse_result
    self.callback, ctx, self, value)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 78, in invoke_param_callback
    return callback(ctx, param, value)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 809, in show_help
    echo(ctx.get_help(), color=ctx.color)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 496, in get_help
    return self.command.get_help(self)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 830, in get_help
    self.format_help(ctx, formatter)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 845, in format_help
    self.format_options(ctx, formatter)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 956, in format_options
    self.format_commands(ctx, formatter)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 1000, in format_commands
    for subcommand in self.list_commands(ctx):
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/commands.py", line 69, in list_commands
    plugins = sorted(self._plugin_lookup)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/commands.py", line 53, in _plugin_lookup
    import q2cli.cache
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 306, in <module>
    CACHE = DeploymentCache()
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 107, in _get_cached_state
    self._cache_current_state(current_requirements)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 200, in _cache_current_state
    state = self._get_current_state()
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/cache.py", line 238, in _get_current_state
    plugin_manager = qiime2.sdk.PluginManager()
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__
    self._init()
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 58, in _init
    plugin = entry_point.load()
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2258, in load
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2264, in resolve
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_feature_classifier/__init__.py", line 15, in <module>
    importlib.import_module('q2_feature_classifier.classifier')
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py", line 251, in <module>
    _register_fitter(name, pipeline)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py", line 215, in _register_fitter
    parameters, signature_params = _pipeline_signature(spec)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py", line 194, in _pipeline_signature
    pipeline = pipeline_from_spec(spec)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py", line 86, in pipeline_from_spec
    steps = json.loads(json.dumps(spec), object_hook=as_steps)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/json/__init__.py", line 332, in loads
    return cls(**kw).decode(s)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/json/decoder.py", line 355, in raw_decode
    obj, end = self.scan_once(s, idx)
  File "/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py", line 83, in as_steps
    return klass(**{k: v for k, v in obj.items() if k != '__type__'})
TypeError: __init__() got an unexpected keyword argument 'alternate_sign'

No. This is how it looks my sys.path within the environment.

['', '/home/william/miniconda3/envs/qiime2-2017.8/lib/python35.zip', '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5', '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/plat-linux', '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/lib-dynload', '/home/william/.local/lib/python3.5/site-packages', '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages', '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg', '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/gneiss-0.4.1-py3.5.egg', '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/ijson-2.3-py3.5.egg', '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg', '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/tzlocal-1.3-py3.5.egg']

Yes, both failed.

Nomkl is not listed with pip freeze. If I compare the conda list with the pip freeze list from my env, multiple packages aren't listed (e.g., Boost v1.61.0, glib v2.50.2, etc.). But I am not sure if it should be the case.

(qiime2-2017.8) william@genobacter:~$ pip freeze
anvio==2.3.1
biom-format==2.1.5
bkcharts==0.2
bleach==1.5.0
bokeh==0.12.7
bottle==0.12.13
CacheControl==0.12.3
CherryPy==8.9.1
click==6.7
cycler==0.10.0
Cython==0.25.2
deblur==1.0.2
decorator==4.1.2
Django==1.11
emperor==1.0.0b8
entrypoints==0.2.3
ete3==3.0.0b35
fastcluster==1.1.23
future==0.16.0
gneiss==0.4.1
h5py==2.7.0
html5lib==0.9999999
ijson==2.3
ipykernel==4.6.1
ipython==6.1.0
ipython-genutils==0.2.0
ipywidgets==6.0.0
jedi==0.10.2
Jinja2==2.9.6
jsonschema==2.6.0
jupyter-client==5.1.0
jupyter-core==4.3.0
lockfile==0.12.2
MarkupSafe==1.0
matplotlib==2.0.2
mistune==0.7.4
msgpack-python==0.4.8
natsort==5.1.0
nbconvert==5.2.1
nbformat==4.4.0
nose==1.3.7
notebook==5.0.0
numpy==1.13.1
pandas==0.20.3
pandocfilters==1.4.2
patsy==0.4.1
pexpect==4.2.1
pickleshare==0.7.4
prompt-toolkit==1.0.15
psutil==5.2.2
ptyprocess==0.5.2
Pygments==2.2.0
pyparsing==2.2.0
pysam==0.11.1
python-dateutil==2.6.1
pytz==2017.2
PyYAML==3.12
pyzmq==16.0.2
q2-alignment==2017.8.0
q2-composition==2017.8.0
q2-dada2==2017.8.0
q2-deblur==2017.8.0
q2-demux==2017.8.0
q2-diversity==2017.8.0
q2-emperor==2017.8.0
q2-feature-classifier==2017.8.0
q2-feature-table==2017.8.0
q2-gneiss==2017.8.0
q2-longitudinal==2017.8.0
q2-metadata==2017.8.0
q2-phylogeny==2017.8.0
q2-quality-filter==2017.8.0
q2-sample-classifier==2017.8.0
q2-taxa==2017.8.0
q2-types==2017.8.0
q2cli==2017.8.0
q2templates==2017.8.0
qiime2==2017.8.0
requests==2.13.0
scikit-bio==0.5.1
scikit-learn==0.18.1
scipy==0.19.0
seaborn==0.8
simplegeneric==0.8.1
six==1.10.0
statsmodels==0.8.0
terminado==0.6
testpath==0.3
tornado==4.5.2
traitlets==4.3.2
tzlocal==1.3
virtualenv==15.1.0
wcwidth==0.1.7
widgetsnbextension==3.0.2

(qiime2-2017.8) william@genobacter:~$ lscpu
Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                24
On-line CPU(s) list:   0-23
Thread(s) per core:    2
Core(s) per socket:    6
Socket(s):             2
NUMA node(s):          2
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 63
Model name:            Intel(R) Xeon(R) CPU E5-2620 v3 @ 2.40GHz
Stepping:              2
CPU MHz:               1204.968
CPU max MHz:           3200.0000
CPU min MHz:           1200.0000
BogoMIPS:              4790.14
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              15360K
NUMA node0 CPU(s):     0-5,12-17
NUMA node1 CPU(s):     6-11,18-23
Flags:                 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm epb tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc dtherm ida arat pln pts
(qiime2-2017.8) william@genobacter:~$ 
(qiime2-2017.8) william@genobacter:~$ uname --all
Linux genobacter 4.4.0-75-generic #96-Ubuntu SMP Thu Apr 20 09:56:33 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

The latter, which is a computer in our lab. I'm connected via ssh. I don't know if the connection mode matters.

Once again thank you for all this effort!

1 Like
12

I think you may have saved the day with sys.path! There's a directory in there that isn't a part of the conda virtual environment (and even comes first, meaning it will override the environment):

/home/william/.local/lib/python3.5/site-packages

I'm not sure how, but that directory is getting added to your sys.path, and it shouldn't be there when you are in a conda environment.

To check this theory, what does:

ls /home/william/.local/lib/python3.5/site-packages

say?

Sorry I should have been more clear, I just wanted to know whether your environment was "2017.8" or "2017.8+nomkl" doesn't matter either way, and it sounds like the latter. As to the missing packages, conda installs binaries in addition to Python packages, so what you've listed are expected to be missing from the pip freeze which only knows of Python.

All that said, there are definitely some things different between our pip-freezes:

What's super cool about this is it is consistent with your two errors. Here's what's happening:

  1. You install QIIME 2 normally (this has Intel MKL optimizations, which you generally want)
  2. Numpy and Scipy are both compiled against a special ABI to make MKL work
  3. Python's import loaders are greedy, as soon as they see a package with the right name, they'll load it and stop looking.
  4. Because you've got .local/lib/python3.5/site-packages in sys.path before the environment's site-packages, it loads a slightly different kind of numpy (same version, but different build)
  5. The ABIs don't match up and so it doesn't load.

We install nomkl, this get's rid of all of the Intel optimisations and uses openblas isntead:

  1. the ABI matches again, so it doesn't have any issues loading
  2. Our scikit-learn is still old (because of the greedy loading), and there was an API break between 0.18.1 and 0.19.0 so now q2-feature-classifier fails to load

So the problem now is going to be figuring out what is changing your sys.path. To confirm:

echo $PYTHONPATH

doesn't say anything?

Right now I'm guessing the way anvio was installed has something to do with it. Do you know what kind of installation you did for Anvi'o?

Thank you for providing so much detail! It really makes this a whole lot simpler!

2 Likes
14

Just noticed you've got virtualenv installed as well. conda and virtualenv don't play super well together, so that may also have something to do with it.

1 Like
15

Sorry for late response, but my remote connection was blocked until recent. It seems download +200GB away from campus place me on "the bad list". @ebolyen I bet your theory is totally right, but I'm having problems to prove it. I guess due to my ignorance with troubleshooting.

Any ways the following command,

shows this,

 (qiime2-2017.8) william@genobacter:~$ ls /home/william/.local/lib/python3.5/site-packages
anvio                     CherryPy-8.9.1.dist-info  Django-1.11.dist-info    mistune                  __pycache__             pyximport                      scipy-0.19.0.dist-info  virtualenv-15.1.0.dist-info
anvio-2.3.1.dist-info     Cython                    ete3                     mistune-0.7.4.dist-info  pysam                   requests                       six-1.10.0.dist-info    virtualenv.py
bottle-0.12.13.dist-info  Cython-0.25.2.dist-info   ete3-3.0.0b35.dist-info  mistune.py               pysam-0.11.1.dist-info  requests-2.13.0.dist-info      six.py                  virtualenv_support
bottle.py                 cython.py                 h5py                     psutil                   pytz                    scikit_learn-0.18.1.dist-info  sklearn
cherrypy                  django                    h5py-2.7.0.dist-info     psutil-5.2.2.dist-info   pytz-2017.2.dist-info   scipy                          tests

echo $PYTHONPATH return empty.

I assume it means the sys.path has been changed by other means. After removing virtualenv (i.e., pip uninstall virtualenv), I uninstall Anvi'o too. However, the sys.path keep showing that odd path, which has anvio in it. I tried to identify from where sys.path source this, but no luck. I tried to debug this problem by looking at the stdout from python -v -m sys within the conda env, which is included below. I ran out of ideas in trying to adjust for that sys.path.

(qiime2-2017.8) william@genobacter:~$ python -v -m sys
import _frozen_importlib # frozen
import _imp # builtin
import sys # builtin
import '_warnings' # <class '_frozen_importlib.BuiltinImporter'>
import '_thread' # <class '_frozen_importlib.BuiltinImporter'>
import '_weakref' # <class '_frozen_importlib.BuiltinImporter'>
import '_frozen_importlib_external' # <class '_frozen_importlib.FrozenImporter'>
import '_io' # <class '_frozen_importlib.BuiltinImporter'>
import 'marshal' # <class '_frozen_importlib.BuiltinImporter'>
import 'posix' # <class '_frozen_importlib.BuiltinImporter'>
import _thread # previously loaded ('_thread')
import '_thread' # <class '_frozen_importlib.BuiltinImporter'>
import _weakref # previously loaded ('_weakref')
import '_weakref' # <class '_frozen_importlib.BuiltinImporter'>
# installing zipimport hook
import 'zipimport' # <class '_frozen_importlib.BuiltinImporter'>
# installed zipimport hook
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/__pycache__/__init__.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/__init__.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/__pycache__/__init__.cpython-35.pyc'
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/codecs.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/codecs.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/codecs.cpython-35.pyc'
import '_codecs' # <class '_frozen_importlib.BuiltinImporter'>
import 'codecs' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e07c940>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/__pycache__/aliases.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/aliases.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/__pycache__/aliases.cpython-35.pyc'
import 'encodings.aliases' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e016438>
import 'encodings' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e07c550>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/__pycache__/utf_8.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/utf_8.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/__pycache__/utf_8.cpython-35.pyc'
import 'encodings.utf_8' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e020208>
import '_signal' # <class '_frozen_importlib.BuiltinImporter'>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/__pycache__/latin_1.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/latin_1.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/__pycache__/latin_1.cpython-35.pyc'
import 'encodings.latin_1' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e020cf8>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/io.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/io.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/io.cpython-35.pyc'
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/abc.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/abc.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/abc.cpython-35.pyc'
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/_weakrefset.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/_weakrefset.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/_weakrefset.cpython-35.pyc'
import '_weakrefset' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e0229b0>
import 'abc' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e0221d0>
import 'io' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e020f28>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/site.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/site.cpython-35.pyc'
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/os.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/os.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/os.cpython-35.pyc'
import 'errno' # <class '_frozen_importlib.BuiltinImporter'>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/stat.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/stat.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/stat.cpython-35.pyc'
import '_stat' # <class '_frozen_importlib.BuiltinImporter'>
import 'stat' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e048f98>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/posixpath.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/posixpath.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/posixpath.cpython-35.pyc'
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/genericpath.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/genericpath.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/genericpath.cpython-35.pyc'
import 'genericpath' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65dfce860>
import 'posixpath' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65dfcb320>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/_collections_abc.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/_collections_abc.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/_collections_abc.cpython-35.pyc'
import '_collections_abc' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65dfceeb8>
import 'os' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e037780>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/_sitebuiltins.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/_sitebuiltins.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/_sitebuiltins.cpython-35.pyc'
import '_sitebuiltins' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e037a58>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/sysconfig.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/sysconfig.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/sysconfig.cpython-35.pyc'
import 'sysconfig' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e001978>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/_sysconfigdata.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/_sysconfigdata.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/_sysconfigdata.cpython-35.pyc'
import '_sysconfigdata' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65df930b8>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/_bootlocale.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/_bootlocale.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/_bootlocale.cpython-35.pyc'
import '_locale' # <class '_frozen_importlib.BuiltinImporter'>
import '_bootlocale' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65df9e128>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/__pycache__/cp437.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/cp437.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/encodings/__pycache__/cp437.cpython-35.pyc'
import 'encodings.cp437' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65dfa5f98>
# zipimport: found 60 names in '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/gneiss-0.4.1-py3.5.egg'
# zipimport: found 23 names in '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/ijson-2.3-py3.5.egg'
# zipimport: found 126 names in '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg'
# zipimport: found 26 names in '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/tzlocal-1.3-py3.5.egg'
import 'site' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65e0332e8>
Python 3.5.4 |Continuum Analytics, Inc.| (default, Aug 14 2017, 13:26:58) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/runpy.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/runpy.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/runpy.cpython-35.pyc'
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/__pycache__/__init__.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/__init__.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/__pycache__/__init__.cpython-35.pyc'
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/types.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/types.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/types.cpython-35.pyc'
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/functools.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/functools.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/functools.cpython-35.pyc'
import '_functools' # <class '_frozen_importlib.BuiltinImporter'>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/collections/__pycache__/__init__.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/collections/__init__.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/collections/__pycache__/__init__.cpython-35.pyc'
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/operator.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/operator.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/operator.cpython-35.pyc'
import '_operator' # <class '_frozen_importlib.BuiltinImporter'>
import 'operator' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c7c14e0>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/keyword.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/keyword.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/keyword.cpython-35.pyc'
import 'keyword' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c7ca668>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/heapq.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/heapq.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/heapq.cpython-35.pyc'
# extension module '_heapq' loaded from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/lib-dynload/_heapq.cpython-35m-x86_64-linux-gnu.so'
# extension module '_heapq' executed from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/lib-dynload/_heapq.cpython-35m-x86_64-linux-gnu.so'
import '_heapq' # <_frozen_importlib_external.ExtensionFileLoader object at 0x7ff65c7cf320>
import 'heapq' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c7caef0>
import 'itertools' # <class '_frozen_importlib.BuiltinImporter'>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/reprlib.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/reprlib.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/reprlib.cpython-35.pyc'
import 'reprlib' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c7cf400>
import '_collections' # <class '_frozen_importlib.BuiltinImporter'>
import 'collections' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c824048>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/weakref.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/weakref.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/weakref.cpython-35.pyc'
import 'weakref' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c824470>
import 'functools' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c80dcf8>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/collections/__pycache__/abc.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/collections/abc.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/collections/__pycache__/abc.cpython-35.pyc'
import 'collections.abc' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c816cc0>
import 'types' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c80d0b8>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/warnings.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/warnings.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/warnings.cpython-35.pyc'
import 'warnings' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c80d160>
import 'importlib' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65dfacd30>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/__pycache__/machinery.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/machinery.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/__pycache__/machinery.cpython-35.pyc'
import 'importlib.machinery' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c81a470>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/__pycache__/util.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/util.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/__pycache__/util.cpython-35.pyc'
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/__pycache__/abc.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/abc.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/importlib/__pycache__/abc.cpython-35.pyc'
import 'importlib.abc' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c7f0d30>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/contextlib.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/contextlib.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/contextlib.cpython-35.pyc'
import 'contextlib' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c7fee80>
import 'importlib.util' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c7f0550>
# /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/pkgutil.cpython-35.pyc matches /home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/pkgutil.py
# code object from '/home/william/miniconda3/envs/qiime2-2017.8/lib/python3.5/__pycache__/pkgutil.cpython-35.pyc'
import 'pkgutil' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65c585fd0>
import 'runpy' # <_frozen_importlib_external.SourceFileLoader object at 0x7ff65dfac940>
/home/william/miniconda3/envs/qiime2-2017.8/bin/python: No code object available for sys
# clear builtins._
17

That is some excellent debugging, thank you @wrodriguez!

I've just found a PEP which describes the behavior of $HOME/.local/lib/python3.5/.

It turns out that this path is always loaded if it exists, so there isn't exactly a tool that is putting the path there, it is Python itself.

I would therefore recommend installing Anvi'o in its own conda environment, and removing /home/william/.local/lib/python3.5/site-packages from your system (or at least renaming it in case there's other things you realize you need later, appending -backup should be enough to keep it from being loaded).

Hope that helps, and thanks for working with us to figure this out! I didn't know about the .local site-packages!

3 Likes
19

Thank you @ebolyen for your time, now is working!

1 Like
20

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