qiime2-2020.11macOS instalation problem

Hi!
I am trying to install the latest version of QIIME2 (qiime2-2020.11) on MacOS Mojave but keep finding this error:

(qiime2-2020.11) MacBook-Air-de-Natali:~ natali$ conda activate qiime2-2020.11
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 "/opt/miniconda3/envs/qiime2-2020.11/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/click/core.py", line 781, in main
    with self.make_context(prog_name, args, **extra) as ctx:
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/click/core.py", line 700, in make_context
    self.parse_args(ctx, args)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/click/command.py", line 43, in parse_args
    return super().parse_args(ctx, args)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/click/core.py", line 1209, in parse_args
    echo(ctx.get_help(), color=ctx.color)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/click/core.py", line 570, in get_help
    return self.command.get_help(self)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/click/core.py", line 975, in get_help
    self.format_help(ctx, formatter)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/click/core.py", line 1003, in format_help
    self.format_options(ctx, formatter)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/click/command.py", line 157, in format_options
    for subcommand in self.list_commands(ctx):
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/commands.py", line 92, in list_commands
    plugins = sorted(self._plugin_lookup)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
    import q2cli.core.cache
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/core/cache.py", line 406, in <module>
    CACHE = DeploymentCache()
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/core/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
    self._cache_current_state(current_requirements)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/core/cache.py", line 200, in _cache_current_state
    state = self._get_current_state()
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/core/cache.py", line 238, in _get_current_state
    plugin_manager = qiime2.sdk.PluginManager()
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 54, in __new__
    self._init(add_plugins=add_plugins)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 81, in _init
    plugin = entry_point.load()
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2472, in load
    return self.resolve()
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2478, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_diversity/__init__.py", line 11, in <module>
    from ._beta import (beta, beta_phylogenetic, bioenv,
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_diversity/_beta/__init__.py", line 12, in <module>
    from ._visualizer import bioenv, beta_group_significance, mantel, adonis
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_diversity/_beta/_visualizer.py", line 25, in <module>
    from natsort import natsorted
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/natsort/__init__.py", line 3, in <module>
    from natsort.natsort import (
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/natsort/natsort.py", line 688, in <module>
    os_sort_key = os_sort_keygen()
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/natsort/natsort.py", line 650, in os_sort_keygen
    key=key, alg=ns.LOCALE | ns.PATH | ns.IGNORECASE
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/natsort/natsort.py", line 177, in natsort_keygen
    input_transform = utils.input_string_transform_factory(alg)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/natsort/utils.py", line 503, in input_string_transform_factory
    thou=re.escape(get_thousands_sep()), nodecimal=nodecimal
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/site-packages/natsort/compat/locale.py", line 73, in get_thousands_sep
    loc = ".".join(locale.getlocale())
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/locale.py", line 581, in getlocale
    return _parse_localename(localename)
  File "/opt/miniconda3/envs/qiime2-2020.11/lib/python3.6/locale.py", line 490, in _parse_localename
    raise ValueError('unknown locale: %s' % localename)
ValueError: unknown locale: UTF-8

Does anybody have any suggestions to fix this?

:slight_smile:

Hi @Natali_Hernandez - this has to do with the locale settings on your system (basically, the spoken language which is enabled). We need some more info to help you out, please run the following commands and copy-and-paste their results here:

a)

env

b)

defaults read .GlobalPreferences AppleLanguages

c)

locale

Thanks! :qiime2:

Hi,

Here are the results

(qiime2-2020.11) MacBook-Air-de-Natali:~ natali$ env

AS=x86_64-apple-darwin13.4.0-as

LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/opt/miniconda3/envs/qiime2-2020.11/lib -L/opt/miniconda3/envs/qiime2-2020.11/lib

AR=x86_64-apple-darwin13.4.0-ar

RSTUDIO_WHICH_R=/opt/miniconda3/envs/qiime2-2020.11/bin/R

ac_cv_func_malloc_0_nonnull=yes

JAVA_LD_LIBRARY_PATH=/opt/miniconda3/envs/qiime2-2020.11/lib/server

TERM_PROGRAM=Apple_Terminal

ac_cv_func_realloc_0_nonnull=yes

OBJC=x86_64-apple-darwin13.4.0-clang

HOST=x86_64-apple-darwin13.4.0

SHELL=/bin/bash

TERM=xterm-256color

NM=x86_64-apple-darwin13.4.0-nm

PYTHONNOUSERSITE=/opt/miniconda3/envs/qiime2-2020.11/lib/python*/site-packages/

CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem /opt/miniconda3/envs/qiime2-2020.11/include

TMPDIR=/var/folders/k0/c19120d9395chyg4m89wbkpm0000gn/T/

PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff

CONDA_SHLVL=2

Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.atu4w4nuRR/Render

LIPO=x86_64-apple-darwin13.4.0-lipo

CONDA_PROMPT_MODIFIER=(qiime2-2020.11)

TERM_PROGRAM_VERSION=421.1.1

GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=

SIZE=x86_64-apple-darwin13.4.0-size

NMEDIT=x86_64-apple-darwin13.4.0-nmedit

SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk

TERM_SESSION_ID=B46A3CA6-F40E-44A4-B0D2-526EC80279FE

CXX_FOR_BUILD=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-clang++

INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool

SEGEDIT=x86_64-apple-darwin13.4.0-segedit

GFORTRAN=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-gfortran

ARBHOME=/opt/miniconda3/envs/qiime2-2020.11/lib/arb

SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack

USER=natali

CLANGXX=x86_64-apple-darwin13.4.0-clang++

LIBTOOL=x86_64-apple-darwin13.4.0-libtool

CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0

FC_FOR_BUILD=/opt/miniconda3/envs/qiime2-2020.11/bin/-gfortran

CONDA_EXE=/opt/miniconda3/bin/conda

OTOOL=x86_64-apple-darwin13.4.0-otool

SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.8juzlk46uR/Listeners

DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /opt/miniconda3/envs/qiime2-2020.11/include -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments

CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -isystem /opt/miniconda3/envs/qiime2-2020.11/include

CONDA_BUILD_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk

STRINGS=x86_64-apple-darwin13.4.0-strings

CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0

_CE_CONDA=

CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms

CONDA_PREFIX_1=/opt/miniconda3

ARBHOME_BACKUP=

PATH=/opt/miniconda3/envs/qiime2-2020.11/bin:/opt/miniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin

GSETTINGS_SCHEMA_DIR=/opt/miniconda3/envs/qiime2-2020.11/share/glib-2.0/schemas

MESON_ARGS=–buildtype release

DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra -isystem /opt/miniconda3/envs/qiime2-2020.11/include

BUILD=x86_64-apple-darwin13.4.0

LD=x86_64-apple-darwin13.4.0-ld

CONDA_PREFIX=/opt/miniconda3/envs/qiime2-2020.11

F90=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-gfortran

PWD=/Users/natali

JAVA_HOME=/opt/miniconda3/envs/qiime2-2020.11

STRIP=x86_64-apple-darwin13.4.0-strip

CMAKE_ARGS=-DCMAKE_AR=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET= -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk

MPLBACKEND=Agg

F95=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-gfortran

DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /opt/miniconda3/envs/qiime2-2020.11/include -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments

XPC_FLAGS=0x0

F77=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-gfortran

REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding

CXX=x86_64-apple-darwin13.4.0-clang++

CC_FOR_BUILD=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-clang

CLANG=x86_64-apple-darwin13.4.0-clang

_CE_M=

XPC_SERVICE_NAME=0

SHLVL=1

HOME=/Users/natali

FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /opt/miniconda3/envs/qiime2-2020.11/include

CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/miniconda3/envs/qiime2-2020.11/include

_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0

FC=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-gfortran

INDR=x86_64-apple-darwin13.4.0-indr

CONDA_PYTHON_EXE=/opt/miniconda3/bin/python

LOGNAME=natali

build_alias=x86_64-apple-darwin13.4.0

LC_CTYPE=UTF-8

JAVA_HOME_CONDA_BACKUP=

CONDA_DEFAULT_ENV=qiime2-2020.11

DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem /opt/miniconda3/envs/qiime2-2020.11/include

RANLIB=x86_64-apple-darwin13.4.0-ranlib

CMAKE_PREFIX_PATH=:/opt/miniconda3/envs/qiime2-2020.11

CC=x86_64-apple-darwin13.4.0-clang

SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table

host_alias=x86_64-apple-darwin13.4.0

JAVA_LD_LIBRARY_PATH_BACKUP=

LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath /opt/miniconda3/envs/qiime2-2020.11/lib -L/opt/miniconda3/envs/qiime2-2020.11/lib

R_LIBS_USER=/opt/miniconda3/envs/qiime2-2020.11/lib/R/library/

SECURITYSESSIONID=186a7

OBJC_FOR_BUILD=/opt/miniconda3/envs/qiime2-2020.11/bin/x86_64-apple-darwin13.4.0-clang

FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /opt/miniconda3/envs/qiime2-2020.11/include

_=/usr/bin/env

(qiime2-2020.11) MacBook-Air-de-Natali:~ natali$ defaults read .GlobalPreferences AppleLanguages

(

“es-MX”

)

(qiime2-2020.11) MacBook-Air-de-Natali:~ natali$ locale

LANG=

LC_COLLATE=“C”

LC_CTYPE=“UTF-8”

LC_MESSAGES=“C”

LC_MONETARY=“C”

LC_NUMERIC=“C”

LC_TIME=“C”

LC_ALL=

Thank you!

Hi @Natali_Hernandez,

Are you able to activate your QIIME 2 enviroment if you prefix the command with LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8, i.e., instead of typing just conda activate qiime2-2020.11 and pressing enter, try:

LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8 conda activate qiime2-2020.11 and press enter.

1 Like

Hi Andrew,

This fixed the problem. Thank you so much! :slight_smile:

1 Like