Trouble with QIIME2 installation on Mac OS (High Sierra)

The installation process does not present issues. I can start QIIME2 but I can run any commands. If I run “qiime --help”, for instance, I get “help requested for activate”.

I’ve tried to clean it up, per instructions and reinstall - same issue. I also reinstalled Miniconda (that’s version 3) with no luck.

Any ideas? More info below. Thanks ahead of time!

wifi-131-179-44-154:~ Wellington$ conda env list

conda environments:

base * /Users/Wellington/miniconda3
qiime2-2017.12 /Users/Wellington/miniconda3/envs/qiime2-2017.12

wifi-131-179-44-154:~ Wellington$ conda info

 active environment : None
        shell level : 0
   user config file : /Users/Wellington/.condarc

populated config files :
conda version : 4.4.8
conda-build version : not installed
python version : 3.6.3.final.0
base environment : /Users/Wellington/miniconda3 (writable)
channel URLs : https://repo.continuum.io/pkgs/main/osx-64
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package cache : /Users/Wellington/miniconda3/pkgs
/Users/Wellington/.conda/pkgs
envs directories : /Users/Wellington/miniconda3/envs
/Users/Wellington/.conda/envs
platform : osx-64
user-agent : conda/4.4.8 requests/2.18.4 CPython/3.6.3 Darwin/17.4.0 OSX/10.13.3
UID:GID : 501:20
netrc file : None
offline mode : False

wifi-131-179-44-154:~ Wellington$ source activate qiime2-2017.12
(qiime2-2017.12) wifi-131-179-44-154:~ Wellington$ conda list

packages in environment at /Users/Wellington/miniconda3/envs/qiime2-2017.12:

Name Version Build Channel

appnope 0.1.0 py35_0 conda-forge
asn1crypto 0.22.0 py35_0 conda-forge
backports 1.0 py35_1 conda-forge
backports.functools_lru_cache 1.4 py35_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 1.14.0 r3.4.1_0 bioconda
bioconductor-genomicranges 1.30.0 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 1.1 openblas conda-forge
blast 2.6.0 boost1.64_2 bioconda
bleach 2.0.0 py_1 conda-forge
bokeh 0.12.13 py35_0 conda-forge
ca-certificates 2017.11.5 0 conda-forge
cachecontrol 0.12.3 py35_0
cairo 1.14.6 4 conda-forge
certifi 2017.11.5 py35_0 conda-forge
cffi 1.11.2 py35_0 conda-forge
chardet 3.0.4 py35_0 conda-forge
clangdev 5.0.0 default_0 conda-forge
click 6.7 py_1 conda-forge
cryptography 2.1.4 py35_0 conda-forge
curl 7.54.1 0 conda-forge
cutadapt 1.15 py35_0 bioconda
cycler 0.10.0 py35_0 conda-forge
cython 0.27.3 py35_0 conda-forge
deblur 1.0.3 py35h7f3a046_0 biocore
decorator 4.1.2 py35_0 conda-forge
emperor 1.0.0beta13 py35_1 conda-forge
entrypoints 0.2.3 py35_1 conda-forge
fastcluster 1.1.24 py35_0 conda-forge
fasttree 2.1.10 0 bioconda
fontconfig 2.12.1 6 conda-forge
freetype 2.7 1 conda-forge
future 0.16.0 py35_0 conda-forge
gettext 0.19.8.1 0 conda-forge
glib 2.51.4 0 conda-forge
gneiss 0.4.2 py35hd262515_6 biocore
graphite2 1.3.10 0 conda-forge
gsl 2.1 2 conda-forge
h5py 2.7.0 np112py35_0 conda-forge
harfbuzz 1.4.3 0 conda-forge
hdf5 1.8.17 11 conda-forge
html5lib 1.0.1 py_0 conda-forge
icu 58.2 0 conda-forge
idna 2.6 py35_1 conda-forge
ijson 2.3 py35_0 qiime2
intel-openmp 2018.0.0 h8158457_8
ipykernel 4.7.0 py35_0 conda-forge
ipython 6.2.1 py35_1 conda-forge
ipython_genutils 0.2.0 py35_0 conda-forge
ipywidgets 7.1.0 py35_0 conda-forge
jedi 0.10.2 py35_0 conda-forge
jinja2 2.10 py35_0 conda-forge
jpeg 9b 2 conda-forge
jsonschema 2.6.0 py35_1 conda-forge
jupyter_client 5.2.1 py35_0 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
krb5 1.14.2 0 conda-forge
libcxx 5.0.0 0 conda-forge
libffi 3.2.1 3 conda-forge
libgcc 4.8.5 hdbeacc1_10
libgfortran 3.0.1 h93005f0_2
libiconv 1.15 0 conda-forge
libpng 1.6.28 1 conda-forge
libsodium 1.0.15 1 conda-forge
libssh2 1.8.0 1 conda-forge
libtiff 4.0.7 0 conda-forge
libxml2 2.9.5 0 conda-forge
llvmdev 5.0.0 default_0 conda-forge
lockfile 0.12.2 py35_0 conda-forge
mafft 7.310 0 bioconda
markupsafe 1.0 py35_0 conda-forge
matplotlib 2.1.1 py35_0 conda-forge
mistune 0.8.3 py_0 conda-forge
mkl 2018.0.1 hfbd8650_4
msgpack-python 0.4.8 py35_0 conda-forge
natsort 5.0.2 py35_0 conda-forge
nbconvert 5.3.1 py_1 conda-forge
nbformat 4.4.0 py35_0 conda-forge
ncurses 5.9 10 conda-forge
nose 1.3.7 py35_2 conda-forge
notebook 5.2.2 py35_1 conda-forge
numpy 1.12.1 py35_blas_openblas_200 [blas_openblas] conda-forge
openblas 0.2.19 2 conda-forge
openjdk 8.0.121 zulu8.20.0.5_0 conda-forge
openssl 1.0.2n 0 conda-forge
pandas 0.22.0 py35_0 conda-forge
pandoc 2.1.1 0 conda-forge
pandocfilters 1.4.1 py35_0 conda-forge
pango 1.40.4 0 conda-forge
patsy 0.5.0 py35_0 conda-forge
pcre 8.39 0 conda-forge
pexpect 4.3.1 py35_0 conda-forge
pickleshare 0.7.4 py35_0 conda-forge
pigz 2.3.4 0 conda-forge
pip 9.0.1 py35_1 conda-forge
pixman 0.34.0 1 conda-forge
prompt_toolkit 1.0.15 py35_0 conda-forge
psutil 5.4.0 py35_0 conda-forge
ptyprocess 0.5.2 py35_0 conda-forge
pycparser 2.18 py35_0 conda-forge
pygments 2.2.0 py35_0 conda-forge
pyopenssl 17.4.0 py35_0 conda-forge
pyparsing 2.2.0 py35_0 conda-forge
pysocks 1.6.7 py35_0 conda-forge
python 3.5.4 0 conda-forge
python-dateutil 2.6.1 py35_0 conda-forge
pytz 2017.3 py_2 conda-forge
pyyaml 3.12 py35_1 conda-forge
pyzmq 16.0.2 py35_3 conda-forge
q2-alignment 2017.12.0 py35_0 qiime2/label/r2017.12
q2-composition 2017.12.0 py35_0 qiime2/label/r2017.12
q2-cutadapt 2017.12.0 py35_0 qiime2/label/r2017.12
q2-dada2 2017.12.1 py35_0 qiime2/label/r2017.12
q2-deblur 2017.12.0 py35_0 qiime2/label/r2017.12
q2-demux 2017.12.0 py35_0 qiime2/label/r2017.12
q2-diversity 2017.12.0 py35_0 qiime2/label/r2017.12
q2-emperor 2017.12.0 py35_0 qiime2/label/r2017.12
q2-feature-classifier 2017.12.0 py35_0 qiime2/label/r2017.12
q2-feature-table 2017.12.0 py35_0 qiime2/label/r2017.12
q2-gneiss 2017.12.0 py35_0 qiime2/label/r2017.12
q2-longitudinal 2017.12.0 py35_0 qiime2/label/r2017.12
q2-metadata 2017.12.0 py35_0 qiime2/label/r2017.12
q2-phylogeny 2017.12.0 py35_0 qiime2/label/r2017.12
q2-quality-control 2017.12.0 py35_0 qiime2/label/r2017.12
q2-quality-filter 2017.12.0 py35_0 qiime2/label/r2017.12
q2-sample-classifier 2017.12.0 py35_0 qiime2/label/r2017.12
q2-taxa 2017.12.0 py35_0 qiime2/label/r2017.12
q2-types 2017.12.0 py35_0 qiime2/label/r2017.12
q2-vsearch 2017.12.0 py35_0 qiime2/label/r2017.12
q2cli 2017.12.0 py35_0 qiime2/label/r2017.12
q2templates 2017.12.0 py35_0 qiime2/label/r2017.12
qiime2 2017.12.1 py35_0 qiime2/label/r2017.12
r-base 3.4.1 0 conda-forge
r-bh 1.65.0_1 r3.4.1_0 conda-forge
r-bitops 1.0_6 r3.4.1_0 conda-forge
r-colorspace 1.3_2 r3.4.1_0 conda-forge
r-data.table 1.10.4 r3.4.1_0 conda-forge
r-dichromat 2.0_0 r3.4.1_0 conda-forge
r-digest 0.6.12 r3.4.1_0 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-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 1.1.9 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 0.2.0 r3.4.1_0 conda-forge
r-magrittr 1.5 r3.4.1_0 conda-forge
r-mass 7.3_45 r3.4.1_0 conda-forge
r-matrix 1.2_7.1 r3.4.1_0 conda-forge
r-matrixstats 0.52.2 r3.4.1_0 conda-forge
r-munsell 0.4.3 r3.4.1_0 conda-forge
r-plyr 1.8.4 r3.4.1_0 conda-forge
r-rcolorbrewer 1.1_2 r3.4.1_0 conda-forge
r-rcpp 0.12.13 r3.4.1_0 conda-forge
r-rcppparallel 4.3.20 r3.4.1_0 conda-forge
r-rcurl 1.95_4.8 r3.4.1_0 conda-forge
r-reshape2 1.4.2 r3.4.1_0 conda-forge
r-rlang 0.1.2 r3.4.1_0 conda-forge
r-scales 0.4.1 r3.4.1_0 conda-forge
r-snow 0.4_2 r3.4.1_0 conda-forge
r-stringi 1.1.5 r3.4.1_0 conda-forge
r-stringr 1.2.0 r3.4.1_0 conda-forge
r-tibble 1.3.3 r3.4.1_0 conda-forge
readline 6.2 0 conda-forge
requests 2.18.4 py35_1 conda-forge
scikit-bio 0.5.1 py35_0 qiime2
scikit-learn 0.19.1 py35_blas_openblas_200 [blas_openblas] conda-forge
scipy 0.19.1 py35_blas_openblas_202 [blas_openblas] conda-forge
seaborn 0.8.1 py35_0 conda-forge
setuptools 38.4.0 py35_0 conda-forge
simplegeneric 0.8.1 py35_0 conda-forge
six 1.11.0 py35_1 conda-forge
sortmerna 2.0 1 bioconda
sqlite 3.13.0 1 conda-forge
statsmodels 0.8.0 py35_0 conda-forge
terminado 0.8.1 py35_0 conda-forge
testpath 0.3.1 py35_0 conda-forge
tk 8.5.19 2 conda-forge
tornado 4.5.2 py35_0 conda-forge
traitlets 4.3.2 py35_0 conda-forge
tzlocal 1.3 py35_0 qiime2
unifrac 0.9.2 py35h1806a49_1 biocore
urllib3 1.22 py35_0 conda-forge
vsearch 2.6.0 0 bioconda
wcwidth 0.1.7 py35_0 conda-forge
webencodings 0.5 py35_0 conda-forge
wget 1.18 0
wheel 0.30.0 py35_2 conda-forge
widgetsnbextension 3.1.0 py35_0 conda-forge
xopen 0.3.2 py35_0 bioconda
xz 5.2.3 0 conda-forge
yaml 0.1.7 0 conda-forge
zeromq 4.2.1 1 conda-forge
zlib 1.2.8 3 conda-forge
(qiime2-2017.12) wifi-131-179-44-154:~ Wellington$ which qiime
/Users/Wellington/miniconda3/envs/qiime2-2017.12/bin/qiime
(qiime2-2017.12) wifi-131-179-44-154:~ Wellington$ qiime info
activate does not accept more than one argument:
(‘qiime2-2017.12’, ‘info’)

(qiime2-2017.12) wifi-131-179-44-154:~ Wellington$ qiime --help
help requested for activate

Actually. I think I fixed it… just by restarting the computer a second time.

1 Like

Thanks for sharing your solution @wamaral!

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