Virtual box installation of qiime 2018.8

davis22 · November 6, 2018, 4:01pm

testing classifiers.

qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ref_seqs.qza --i-reference-taxonomy ref_taxa.qza --o-classifier nb_classifier.qza

long error…
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2018.8/bin/qiime”, line 11, in
sys.exit(qiime())
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 722, in call
return self.main(*args, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 697, in main
rv = self.invoke(ctx)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 535, in invoke
return callback(*args, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py”, line 244, in call
arguments, missing_in, verbose, quiet = self.handle_in_params(kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py”, line 326, in handle_in_params
kwargs, fallback=cmd_fallback)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/handlers.py”, line 375, in get_value
artifact = qiime2.sdk.Result.load(path)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 65, in load
archiver = archive.Archiver.load(filepath)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/archiver.py”, line 301, in load
return cls(path, Format(rec))
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/format/v1.py”, line 29, in init
super().init(archive_record)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/format/v0.py”, line 72, in init
self.type = sdk.parse_type(type)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/util.py”, line 57, in parse_type
pm = qiime2.sdk.PluginManager()
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py”, line 44, in new
self._init()
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py”, line 59, in _init
plugin = entry_point.load()
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/pkg_resources/init.py”, line 2325, in load
return self.resolve()
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/pkg_resources/init.py”, line 2331, in resolve
module = import(self.module_name, fromlist=[‘name’], level=0)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_vsearch/plugin_setup.py”, line 12, in
import q2_vsearch._cluster_features
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_vsearch/_cluster_features.py”, line 15, in
import skbio
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/init.py”, line 13, in
import skbio.io # noqa
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/io/init.py”, line 248, in
import_module(‘skbio.io.format.lsmat’)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/importlib/init.py”, line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/io/format/lsmat.py”, line 77, in
from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/stats/distance/init.py”, line 193, in
from ._base import (DissimilarityMatrixError, DistanceMatrixError,
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/stats/distance/_base.py”, line 12, in
from IPython.core.pylabtools import print_figure
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/IPython/init.py”, line 55, in
from .terminal.embed import embed
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/IPython/terminal/embed.py”, line 16, in
from IPython.terminal.interactiveshell import TerminalInteractiveShell
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/IPython/terminal/interactiveshell.py”, line 22, in
from prompt_toolkit.shortcuts import create_prompt_application, create_eventloop, create_prompt_layout, create_output
ImportError: cannot import name ‘create_prompt_application’

Any ideas?

Thanks Denise

lca123 · November 7, 2018, 11:27am

I am getting similar error from 2 days ago. It poped up after two commands: 1) a classifier command; 2) an export command. To note: those commands were working fine recently.

(running Qiime2-2018.6 here)

qiime feature-classifier classify-consensus-vsearch \
     --i-query rep-seqs.qza \
     --i-reference-reads reference.silva.qza \
     --i-reference-taxonomy taxonomy.silva.qza \
     --p-maxaccepts 1 \
     --p-perc-identity 0.99 \
     --p-threads 14 \
     --output-dir out_vsearch \
     --o-classification out_vsearch/classification.qza

qiime tools export --output-dir . rep-seqs.qza

Error:
Traceback (most recent call last):
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/bin/qiime", line 11, in
sys.exit(qiime())
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py", line 244, in call
arguments, missing_in, verbose, quiet = self.handle_in_params(kwargs)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py", line 326, in handle_in_params
kwargs, fallback=cmd_fallback)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/handlers.py", line 375, in get_value
artifact = qiime2.sdk.Result.load(path)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/result.py", line 65, in load
archiver = archive.Archiver.load(filepath)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 301, in load
return cls(path, Format(rec))
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/core/archive/format/v1.py", line 29, in init
super().init(archive_record)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/core/archive/format/v0.py", line 72, in init
self.type = sdk.parse_type(type)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/util.py", line 57, in parse_type
pm = qiime2.sdk.PluginManager()
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in new
self._init()
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 59, in _init
plugin = entry_point.load()
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/pkg_resources/init.py", line 2318, in load
return self.resolve()
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/pkg_resources/init.py", line 2324, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_vsearch/plugin_setup.py", line 12, in
import q2_vsearch._cluster_features
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_vsearch/_cluster_features.py", line 15, in
import skbio
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/skbio/init.py", line 13, in
import skbio.io # noqa
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/skbio/io/init.py", line 238, in
import_module('skbio.io.format.lsmat')
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/skbio/io/format/lsmat.py", line 77, in
from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/skbio/stats/distance/init.py", line 192, in
from ._base import (DissimilarityMatrixError, DistanceMatrixError,
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 13, in
from IPython.core.pylabtools import print_figure
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/IPython/init.py", line 55, in
from .terminal.embed import embed
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/IPython/terminal/embed.py", line 16, in
from IPython.terminal.interactiveshell import TerminalInteractiveShell
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/IPython/terminal/interactiveshell.py", line 22, in
from prompt_toolkit.shortcuts import create_prompt_application, create_eventloop, create_prompt_layout, create_output
ImportError: cannot import name 'create_prompt_application'

Maybe there is something related to Jupyter? I don't know if Qiime2-2018.8 is Jupiter-related at some point, but 2 days ago I installed tax-credit and them this error began to come up.

git clone https://github.com/gregcaporaso/tax-credit.git
cd tax-credit/
pip install .

This thread mention the error with Jupiter:

github.com/jupyter/jupyter_console

Jupyter-console incompatible with prompt-toolkit 2.0.2

opened 12:39PM - 08 Jun 18 UTC

closed 11:02PM - 03 Oct 18 UTC

blfuentes

After updating the prompt-toolkit package to the version 2.0.2 I get the followi…ng error message : `jupyter-console 5.2.0 has requirement prompt-toolkit<2.0.0,>=1.0.0, but you'll have prompt-toolkit 2.0.2 which is incompatible.` Then if I start a jupyter notebook the message "kernel died" is appearing all the time with this output ``` [I 14:23:58.331 NotebookApp] Kernel started: 60ff14ae-6730-43b2-9c9a-5df4b549aa03 Traceback (most recent call last): File "c:\program files (x86)\microsoft visual studio\shared\python36_64\lib\runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "c:\program files (x86)\microsoft visual studio\shared\python36_64\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "c:\program files (x86)\microsoft visual studio\shared\python36_64\lib\site-packages\ipykernel_launcher.py", line 15, in <module> from ipykernel import kernelapp as app File "c:\program files (x86)\microsoft visual studio\shared\python36_64\lib\site-packages\ipykernel\__init__.py", line 2, in <module> from .connect import * File "c:\program files (x86)\microsoft visual studio\shared\python36_64\lib\site-packages\ipykernel\connect.py", line 13, in <module> from IPython.core.profiledir import ProfileDir File "c:\program files (x86)\microsoft visual studio\shared\python36_64\lib\site-packages\IPython\__init__.py", line 55, in <module> from .terminal.embed import embed File "c:\program files (x86)\microsoft visual studio\shared\python36_64\lib\site-packages\IPython\terminal\embed.py", line 16, in <module> from IPython.terminal.interactiveshell import TerminalInteractiveShell File "c:\program files (x86)\microsoft visual studio\shared\python36_64\lib\site-packages\IPython\terminal\interactiveshell.py", line 22, in <module> from prompt_toolkit.shortcuts import create_prompt_application, create_eventloop, create_prompt_layout, create_output ImportError: cannot import name 'create_prompt_application' [I 14:24:01.294 NotebookApp] KernelRestarter: restarting kernel (1/5), new random ports ``` I downgraded the prompt-toolkit to the version 1.0.15 and jupyter worked again. Python 3.6.5 jupyter 1.0.0 jupyter-client 5.2.3 jupyter-console 5.2.0 jupyter-core 4.4.0 ipython 6.4.0

Nicholas_Bokulich · November 7, 2018, 1:04pm

thermokarst · November 8, 2018, 1:45am

Hey there @lca123. In your QIIME 2 env can you please run the following and provide the results?

conda info

and

conda list

Thanks!

thermokarst · November 8, 2018, 1:45am

lca123 · November 8, 2018, 11:04am

Hey there, @thermokarst
There you go.
Thanks!

$ conda info

     active environment : qiime2-2018.6
    active env location : /home/leonardo.alves/miniconda2/envs/qiime2-2018.6
            shell level : 1
       user config file : /home/leonardo.alves/.condarc
 populated config files :
          conda version : 4.5.9
    conda-build version : not installed
         python version : 2.7.15.final.0
       base environment : /home/leonardo.alves/miniconda2  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /home/leonardo.alves/miniconda2/pkgs
                          /home/leonardo.alves/.conda/pkgs
       envs directories : /home/leonardo.alves/miniconda2/envs
                          /home/leonardo.alves/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.9 requests/2.18.4 CPython/2.7.15 Linux/3.10.0-693.el7.x86_64 centos/7 glibc/2.17
                UID:GID : 1001:1001
             netrc file : None
           offline mode : False
 


$ conda list
# packages in environment at /home/leonardo.alves/miniconda2/envs/qiime2-2018.6:
#
# Name                    Version                   Build  Channel
asn1crypto                0.24.0                     py_1    conda-forge
backcall                  0.1.0                      py_0    conda-forge
bibtexparser              1.0.1                      py_1    conda-forge
bioconductor-biobase      2.38.0                 r3.4.1_0    bioconda
bioconductor-biocgenerics 0.24.0                 r3.4.1_0    bioconda
bioconductor-biocparallel 1.12.0                 r3.4.1_0    bioconda
bioconductor-biostrings   2.46.0                 r3.4.1_0    bioconda
bioconductor-dada2        1.6.0                  r3.4.1_0    bioconda
bioconductor-delayedarray 0.4.1                  r3.4.1_0    bioconda
bioconductor-genomeinfodb 1.14.0                 r3.4.1_0    bioconda
bioconductor-genomeinfodbdata 1.0.0                  r3.4.1_1    bioconda
bioconductor-genomicalignments 1.14.1                 r3.4.1_0    bioconda
bioconductor-genomicranges 1.30.3                 r3.4.1_0    bioconda
bioconductor-iranges      2.12.0                 r3.4.1_0    bioconda
bioconductor-rsamtools    1.30.0                 r3.4.1_0    bioconda
bioconductor-s4vectors    0.16.0                 r3.4.1_0    bioconda
bioconductor-shortread    1.36.0                 r3.4.1_0    bioconda
bioconductor-summarizedexperiment 1.8.0                  r3.4.1_0    bioconda
bioconductor-xvector      0.18.0                 r3.4.1_0    bioconda
bioconductor-zlibbioc     1.24.0                 r3.4.1_0    bioconda
biom-format               2.1.6                    py35_8    qiime2
blas                      1.0                         mkl
blast                     2.6.0               boost1.64_2    bioconda
bleach                    2.1.3                      py_0    conda-forge
bokeh                     0.12.15                  py35_0    conda-forge
boost                     1.64.0                   py35_4    conda-forge
boost-cpp                 1.64.0                        1    conda-forge
bz2file                   0.98                     py35_0
bzip2                     1.0.6                h470a237_2    conda-forge
ca-certificates           2018.4.16                     0    conda-forge
cachecontrol              0.12.4                     py_0    conda-forge
cairo                     1.14.10                       0    conda-forge
certifi                   2018.4.16                py35_0
cffi                      1.11.5                   py35_0    conda-forge
chardet                   3.0.4                    py35_2    conda-forge
click                     6.7                        py_1    conda-forge
cryptography              2.2.1            py35hdffb7b8_1    conda-forge
curl                      7.60.0                        0    conda-forge
cutadapt                  1.16                     py35_2    bioconda
cycler                    0.10.0                     py_1    conda-forge
cython                    0.28.3           py35hfc679d8_0    conda-forge
dbus                      1.13.0               h3a4f0e9_0    conda-forge
deblur                    1.0.4                    py35_2    bioconda
decorator                 4.3.0                      py_0    conda-forge
emperor                   1.0.0beta16              py35_1    conda-forge
entrypoints               0.2.3                    py35_1    conda-forge
expat                     2.2.5                hfc679d8_1    conda-forge
fastcluster               1.1.25           py35hf8a1672_0    conda-forge
fasttree                  2.1.10               h470a237_2    bioconda
fontconfig                2.12.6                        0    conda-forge
freetype                  2.8.1                hfa320df_1    conda-forge
future                    0.16.0                   py35_2    conda-forge
gettext                   0.19.8.1                      0    conda-forge
glib                      2.55.0               h464dc38_2    conda-forge
gmp                       6.1.2                hfc679d8_0    conda-forge
gneiss                    0.4.4            py27h1cf38a6_1    biocore
graphite2                 1.3.11               hfc679d8_0    conda-forge
gsl                       2.1                           2    conda-forge
gst-plugins-base          1.8.0                         0    conda-forge
gstreamer                 1.8.0                         1    conda-forge
h5py                      2.7.0               np112py35_0    conda-forge
harfbuzz                  1.7.6                         0    conda-forge
hdf5                      1.8.17                       11    conda-forge
html5lib                  1.0.1                      py_0    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
idna                      2.7                      py35_2    conda-forge
ijson                     2.3                      py35_0    qiime2
intel-openmp              2018.0.3                      0
ipykernel                 4.8.2                    py35_0    conda-forge
ipython                   6.4.0                    py35_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.2.1                    py35_1    conda-forge
jedi                      0.12.0                   py35_0    conda-forge
jinja2                    2.10                       py_1    conda-forge
joblib                    0.12.5                    <pip>
jpeg                      9b                   h470a237_3    conda-forge
jsonschema                2.6.0                    py35_1    conda-forge
jupyter_client            5.2.3                      py_1    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
kiwisolver                1.0.1                    py35_1    conda-forge
krb5                      1.14.6                        0    conda-forge
libffi                    3.2.1                         3    conda-forge
libgcc                    7.2.0                h69d50b8_2
libgcc-ng                 7.2.0                hdf63c60_3
libgfortran               3.0.0                         1
libgfortran-ng            7.2.0                hdf63c60_3
libiconv                  1.15                 h470a237_1    conda-forge
libpng                    1.6.34               ha92aebf_1    conda-forge
libsodium                 1.0.16                        0    conda-forge
libssh2                   1.8.0                h5b517e9_2    conda-forge
libstdcxx-ng              7.2.0                hdf63c60_3
libtiff                   4.0.9                he6b73bb_1    conda-forge
libxcb                    1.13                 h470a237_2    conda-forge
libxml2                   2.9.8                h422b904_2    conda-forge
lockfile                  0.12.2                     py_1    conda-forge
mafft                     7.310                         1    bioconda
markupsafe                1.0                      py35_0    conda-forge
matplotlib                2.2.2                    py35_1    conda-forge
mistune                   0.8.3            py35h470a237_2    conda-forge
mkl                       2018.0.3                      1
msgpack-python            0.5.6                     <pip>
msgpack-python            0.5.6            py35h2d50403_2    conda-forge
natsort                   5.3.2                      py_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   5.9                          10    conda-forge
nose                      1.3.7                    py35_2    conda-forge
notebook                  5.5.0                    py35_0    conda-forge
numpy                     1.12.1           py35hca0bb5e_1
openblas                  0.2.19                        2    conda-forge
openssl                   1.0.2o               h14c3975_1
packaging                 17.1                       py_0    conda-forge
pandas                    0.23.1                   py35_0    conda-forge
pandoc                    2.2.1                         0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.40.14                       0    conda-forge
parso                     0.2.1                      py_0    conda-forge
patsy                     0.5.0                      py_1    conda-forge
pcre                      8.39                          0    conda-forge
pexpect                   4.6.0                    py35_0    conda-forge
pickleshare               0.7.4                    py35_0    conda-forge
pigz                      2.3.4                         0    conda-forge
pip                       9.0.3                    py35_0    conda-forge
pixman                    0.34.0                        2    conda-forge
prompt-toolkit            2.0.7                     <pip>
prompt_toolkit            1.0.15           py35hc09de7a_0
psutil                    5.4.6                    py35_0    conda-forge
pthread-stubs             0.4                  h470a237_1    conda-forge
ptyprocess                0.6.0                    py35_0    conda-forge
pycparser                 2.18                       py_1    conda-forge
pygments                  2.2.0                      py_1    conda-forge
pyopenssl                 18.0.0                   py35_0    conda-forge
pyparsing                 2.2.0                      py_1    conda-forge
pyqt                      5.6.0            py35h8210e8a_6    conda-forge
pysocks                   1.6.8                    py35_1    conda-forge
python                    3.5.5                         1    conda-forge
python-dateutil           2.7.3                      py_0    conda-forge
pytz                      2018.4                     py_0    conda-forge
pyyaml                    3.12                     py35_1    conda-forge
pyzmq                     17.0.0           py35hae99301_5    conda-forge
q2-alignment              2018.6.0                 py35_0    qiime2/label/r2018.6
q2-composition            2018.6.0                 py35_0    qiime2/label/r2018.6
q2-cutadapt               2018.6.0                 py35_0    qiime2/label/r2018.6
q2-dada2                  2018.6.0                 py35_0    qiime2/label/r2018.6
q2-deblur                 2018.6.0                 py35_0    qiime2/label/r2018.6
q2-demux                  2018.6.0                 py35_0    qiime2/label/r2018.6
q2-diversity              2018.6.0                 py35_0    qiime2/label/r2018.6
q2-emperor                2018.6.0                 py35_0    qiime2/label/r2018.6
q2-feature-classifier     2018.6.0                 py35_0    qiime2/label/r2018.6
q2-feature-table          2018.6.0                 py35_0    qiime2/label/r2018.6
q2-gneiss                 2018.6.0                 py35_0    qiime2/label/r2018.6
q2-longitudinal           2018.6.0                 py35_0    qiime2/label/r2018.6
q2-metadata               2018.6.0                 py35_0    qiime2/label/r2018.6
q2-phylogeny              2018.6.0                 py35_0    qiime2/label/r2018.6
q2-quality-control        2018.6.1                 py35_0    qiime2/label/r2018.6
q2-quality-filter         2018.6.0                 py35_0    qiime2/label/r2018.6
q2-sample-classifier      2018.6.0                 py35_0    qiime2/label/r2018.6
q2-taxa                   2018.6.0                 py35_0    qiime2/label/r2018.6
q2-types                  2018.6.0                 py35_0    qiime2/label/r2018.6
q2-vsearch                2018.6.0                 py35_0    qiime2/label/r2018.6
q2cli                     2018.6.0                 py35_0    qiime2/label/r2018.6
q2templates               2018.6.0                 py35_0    qiime2/label/r2018.6
qiime2                    2018.6.0                 py35_0    qiime2/label/r2018.6
qt                        5.6.2                         7    conda-forge
qtconsole                 4.4.2                     <pip>
r-assertthat              0.2.0                  r3.4.1_0    conda-forge
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r-colorspace              1.3_2            r341h470a237_1    conda-forge
r-crayon                  1.3.4                  r3.4.1_0    conda-forge
r-data.table              1.11.4           r341hc070d10_0    conda-forge
r-dichromat               2.0_0                  r3.4.1_0    conda-forge
r-digest                  0.6.15           r341h470a237_1    conda-forge
r-futile.logger           1.4.3                  r3.4.1_0    conda-forge
r-futile.options          1.0.0                  r3.4.1_0    conda-forge
r-ggplot2                 2.2.1                  r3.4.1_0    conda-forge
r-glue                    1.2.0                  r3.4.1_0    conda-forge
r-gtable                  0.2.0                  r3.4.1_0    conda-forge
r-hwriter                 1.3.2                  r3.4.1_0    conda-forge
r-labeling                0.3                    r3.4.1_0    conda-forge
r-lambda.r                1.2                    r3.4.1_0    conda-forge
r-lattice                 0.20_34                r3.4.1_0    conda-forge
r-latticeextra            0.6_28                 r3.4.1_0    conda-forge
r-lazyeval                0.2.1            r341h470a237_1    conda-forge
r-magrittr                1.5                    r3.4.1_0    conda-forge
r-mass                    7.3_48                 r3.4.1_0    conda-forge
r-matrix                  1.2_14           r341h470a237_1    conda-forge
r-matrixstats             0.53.1           r341h470a237_1    conda-forge
r-munsell                 0.5.0                    r341_0    conda-forge
r-pillar                  1.2.1                  r3.4.1_0    conda-forge
r-plyr                    1.8.4            r341hfc679d8_1    conda-forge
r-r6                      2.2.2                  r3.4.1_0    conda-forge
r-rcolorbrewer            1.1_2                  r3.4.1_0    conda-forge
r-rcpp                    0.12.15                r3.4.1_0    conda-forge
r-rcppparallel            4.4.0            r341hfc679d8_1    conda-forge
r-rcurl                   1.95_4.8               r3.4.1_0    conda-forge
r-reshape2                1.4.3            r341hfc679d8_1    conda-forge
r-rlang                   0.2.1            r341h470a237_1    conda-forge
r-scales                  0.5.0            r341hfc679d8_1    conda-forge
r-snow                    0.4_2                  r3.4.1_0    conda-forge
r-stringi                 1.1.7                  r3.4.1_1    conda-forge
r-stringr                 1.3.0                  r3.4.1_0    conda-forge
r-tibble                  1.4.2            r341h470a237_1    conda-forge
r-utf8                    1.1.3            r341h470a237_1    conda-forge
r-viridislite             0.3.0                  r3.4.1_0    conda-forge
raxml                     8.2.10               h470a237_1    bioconda
readline                  7.0                           0    conda-forge
requests                  2.19.1                   py35_1    conda-forge
scikit-bio                0.5.1                    py35_0    qiime2
scikit-learn              0.19.1           py35hbf1f462_0
scipy                     0.19.1           py35ha8f041b_3
seaborn                   0.8.1                      py_1    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                39.2.0                   py35_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
sip                       4.18                     py35_1    conda-forge
six                       1.11.0                   py35_1    conda-forge
sortmerna                 2.0                  he941832_3    bioconda
sqlite                    3.20.1                        2    conda-forge
statsmodels               0.9.0                    py35_0    conda-forge
tax-credit                0.0.0.dev0                <pip>
terminado                 0.8.1                    py35_0    conda-forge
testpath                  0.3.1                    py35_0    conda-forge
tk                        8.6.7                         0    conda-forge
tornado                   5.0.2                    py35_0    conda-forge
traitlets                 4.3.2                    py35_0    conda-forge
tzlocal                   1.3                      py35_0    qiime2
unifrac                   0.9.2            py35hae32d81_1    biocore
urllib3                   1.23                     py35_0    conda-forge
vsearch                   2.7.0                         1    bioconda
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5                      py35_0    conda-forge
wget                      1.19.5               h1ad7b7a_0
wheel                     0.31.0                   py35_0    conda-forge
widgetsnbextension        3.2.1                    py35_1    conda-forge
xopen                     0.3.2                      py_1    bioconda
xorg-libxau               1.0.8                h470a237_6    conda-forge
xorg-libxdmcp             1.1.2                h470a237_7    conda-forge
xz                        5.2.3                         0    conda-forge
yaml                      0.1.7                         0    conda-forge
zeromq                    4.2.5                hfc679d8_5    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

Nicholas_Bokulich · November 8, 2018, 1:39pm

thermokarst · November 9, 2018, 7:00pm

Hey there @lca123 — it looks like you might’ve uninstalled some dependencies when installing tax-credit. I suggest you stick tax-credit in an all new conda env. Also, I would erase your 2018.6 env and reinstall, since it appears to be corrupt now. Or, better yet, install 2018.11, out now!

thermokarst · November 9, 2018, 7:00pm

lca123 · November 10, 2018, 6:19pm

Many thanks! I’ll follow your suggestions.

system · December 12, 2018, 12:20am

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