Using qiime2 in ipython

Hi,

I have recently installed the newest update of qiime2, 2021.11. I am trying to run qiime2 as a module within ipython. To do so I activate the qiime2 conda environment and enter ipython.

When trying to load qiime2 in ipython (e.g. qiime2.plugins.feature_table.actions as feature_table_actions) I get the error "No module named 'qiime2'

I think I am missing something fundamental

Thanks for any help in advance.

@Maurice_Barrett,

Let's make sure that the correct conda environment is activated by running qiime info and also check that ipython is installed in your environment with conda list.

It sounds like somehow a different install of ipython is coming first in your path, so go ahead and run which ipython as well?

1 Like

Hi @Keegan-Evans, thank you for your reply.

qiime info

System versions
Python version: 3.8.12
QIIME 2 release: 2021.11
QIIME 2 version: 2021.11.0
q2cli version: 2021.11.0

Installed plugins
alignment: 2021.11.0
composition: 2021.11.0
cutadapt: 2021.11.0
dada2: 2021.11.0
deblur: 2021.11.0
demux: 2021.11.0
diversity: 2021.11.0
diversity-lib: 2021.11.0
emperor: 2021.11.0
feature-classifier: 2021.11.0
feature-table: 2021.11.0
fragment-insertion: 2021.11.0
gneiss: 2021.11.0
longitudinal: 2021.11.0
metadata: 2021.11.0
phylogeny: 2021.11.0
quality-control: 2021.11.0
quality-filter: 2021.11.0
sample-classifier: 2021.11.0
taxa: 2021.11.0
types: 2021.11.0
vsearch: 2021.11.0

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
alsa-lib 1.2.3 h516909a_0 conda-forge
argcomplete 1.12.3 pyhd8ed1ab_2 conda-forge
argon2-cffi 21.1.0 py38h497a2fe_2 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 21.2.0 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
bibtexparser 1.1.0 py_0 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_2 conda-forge
bioconductor-biobase 2.50.0 r40hd029910_1 bioconda
bioconductor-biocgenerics 0.36.0 r40hdfd78af_1 bioconda
bioconductor-biocparallel 1.24.1 r40h399db7b_0 bioconda
bioconductor-biostrings 2.58.0 r40hd029910_1 bioconda
bioconductor-dada2 1.18.0 r40h399db7b_1 bioconda
bioconductor-delayedarray 0.16.3 r40hd029910_0 bioconda
bioconductor-genomeinfodb 1.26.4 r40hdfd78af_0 bioconda
bioconductor-genomeinfodbdata 1.2.4 r40hdfd78af_2 bioconda
bioconductor-genomicalignments 1.26.0 r40hd029910_1 bioconda
bioconductor-genomicranges 1.42.0 r40hd029910_1 bioconda
bioconductor-iranges 2.24.1 r40hd029910_0 bioconda
bioconductor-matrixgenerics 1.2.1 r40hdfd78af_0 bioconda
bioconductor-rhtslib 1.22.0 r40hd029910_1 bioconda
bioconductor-rsamtools 2.6.0 r40h399db7b_1 bioconda
bioconductor-s4vectors 0.28.1 r40hd029910_0 bioconda
bioconductor-shortread 1.48.0 r40h399db7b_1 bioconda
bioconductor-summarizedexperiment 1.20.0 r40hdfd78af_1 bioconda
bioconductor-xvector 0.30.0 r40hd029910_1 bioconda
bioconductor-zlibbioc 1.36.0 r40hd029910_1 bioconda
biom-format 2.1.10 py38h6c62de6_1 conda-forge
blast 2.12.0 pl5262h3289130_0 bioconda
bleach 4.1.0 pyhd8ed1ab_0 conda-forge
bokeh 2.4.2 py38h578d9bd_0 conda-forge
bowtie2 2.4.2 py38hc2f83ea_2 bioconda
brotli 1.0.9 h7f98852_6 conda-forge
brotli-bin 1.0.9 h7f98852_6 conda-forge
brotlipy 0.7.0 py38h497a2fe_1003 conda-forge
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
cachecontrol 0.12.10 pyhd8ed1ab_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 h6cf1ce9_1008 conda-forge
certifi 2021.10.8 py38h578d9bd_1 conda-forge
cffi 1.15.0 py38h3931269_0 conda-forge
chardet 4.0.0 py38h578d9bd_2 conda-forge
click 7.1.2 pyh9f0ad1d_0 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
cryptography 35.0.0 py38h3e25421_2 conda-forge
curl 7.80.0 h2574ce0_0 conda-forge
cutadapt 3.5 py38h4a8c8d9_0 bioconda
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.24 py38h709712a_1 conda-forge
dbus 1.13.6 h48d8840_2 conda-forge
deblur 1.1.0 py_2 bioconda
debugpy 1.5.1 py38h709712a_0 conda-forge
decorator 4.4.2 py_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dendropy 4.5.2 pyh3252c3a_0 bioconda
dill 0.3.4 pyhd8ed1ab_0 conda-forge
dnaio 0.6.0 py38h4a8c8d9_0 bioconda
emperor 1.0.3 py38h578d9bd_0 conda-forge
entrez-direct 16.2 he881be0_0 bioconda
entrypoints 0.3 pyhd8ed1ab_1003 conda-forge
expat 2.4.1 h9c3ff4c_0 conda-forge
fastcluster 1.1.26 py38h43a58ef_3 conda-forge
fasttree 2.1.10 0 bioconda
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.13.1 hba837de_1005 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.28.1 py38h497a2fe_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
future 0.18.2 py38h578d9bd_4 conda-forge
gcc_impl_linux-64 9.4.0 h03d3576_11 conda-forge
gcc_linux-64 9.4.0 h391b98a_2 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
gfortran_impl_linux-64 9.4.0 h0003116_11 conda-forge
gfortran_linux-64 9.4.0 hf0ab688_2 conda-forge
glib 2.70.1 h780b84a_0 conda-forge
glib-tools 2.70.1 h780b84a_0 conda-forge
gneiss 0.4.6 py_0 bioconda
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.7 he838d99_0 conda-forge
gst-plugins-base 1.18.5 hf529b03_2 conda-forge
gstreamer 1.18.5 h9f60fe5_2 conda-forge
gxx_impl_linux-64 9.4.0 h03d3576_11 conda-forge
gxx_linux-64 9.4.0 h0316aca_2 conda-forge
h5py 3.3.0 nompi_py38h9915d05_100 conda-forge
harfbuzz 3.1.1 h83ec7ef_0 conda-forge
hdf5 1.10.6 nompi_h6a2412b_1114 conda-forge
hdmedians 0.14.2 py38h6c62de6_1 conda-forge
hmmer 3.1b2 3 bioconda
htslib 1.14 h9093b5e_0 bioconda
icu 68.2 h9c3ff4c_0 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
ijson 3.1.3 pyhd3deb0d_0 conda-forge
importlib-metadata 4.8.2 py38h578d9bd_0 conda-forge
importlib_metadata 4.8.2 hd8ed1ab_0 conda-forge
importlib_resources 5.4.0 pyhd8ed1ab_0 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
ipykernel 6.5.0 py38he5a9106_1 conda-forge
ipython 7.29.0 py38he5a9106_2 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.6.5 pyhd8ed1ab_0 conda-forge
iqtree 2.1.4_beta hdcc8f71_0 bioconda
isa-l 2.30.0 ha770c72_4 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jedi 0.18.1 py38h578d9bd_0 conda-forge
jinja2 3.0.3 pyhd8ed1ab_0 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
jq 1.6 h36c2ea0_1000 conda-forge
jsonschema 4.2.1 pyhd8ed1ab_1 conda-forge
jupyter_client 7.1.0 pyhd8ed1ab_0 conda-forge
jupyter_core 4.9.1 py38h578d9bd_1 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
jupyterlab_widgets 1.0.2 pyhd8ed1ab_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
kiwisolver 1.3.2 py38h1fd1430_1 conda-forge
krb5 1.19.2 hcc1bbae_3 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 2.2.1 h9c3ff4c_0 conda-forge
libblas 3.9.0 12_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h7f98852_6 conda-forge
libbrotlidec 1.0.9 h7f98852_6 conda-forge
libbrotlienc 1.0.9 h7f98852_6 conda-forge
libcblas 3.9.0 12_linux64_openblas conda-forge
libclang 11.1.0 default_ha53f305_1 conda-forge
libcurl 7.80.0 h2574ce0_0 conda-forge
libdeflate 1.7 h7f98852_5 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 h9b69904_4 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-devel_linux-64 9.4.0 hd854feb_11 conda-forge
libgcc-ng 11.2.0 h1d223b6_11 conda-forge
libgfortran-ng 11.2.0 h69a702a_11 conda-forge
libgfortran5 11.2.0 h5c6108e_11 conda-forge
libglib 2.70.1 h174f98d_0 conda-forge
libgomp 11.2.0 h1d223b6_11 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 12_linux64_openblas conda-forge
libllvm10 10.0.1 he513fc3_3 conda-forge
libllvm11 11.1.0 hf817b99_2 conda-forge
libnghttp2 1.43.0 h812cca2_1 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libpq 13.5 hd57d9b9_1 conda-forge
libsanitizer 9.4.0 h79bfe98_11 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-devel_linux-64 9.4.0 hd854feb_11 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_11 conda-forge
libtiff 4.3.0 hf544144_1 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libuv 1.42.0 h7f98852_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.2.1 h7f98852_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.12 h72842e0_0 conda-forge
libxslt 1.1.33 h15afd5d_2 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
llvmlite 0.36.0 py38h4630a5e_0 conda-forge
lockfile 0.12.2 py_1 conda-forge
lxml 4.6.4 py38hf1fe3a4_0 conda-forge
lz4 3.1.3 py38hebdc3cf_1 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
mafft 7.490 h779adbc_0 bioconda
make 4.3 hd18ef5c_1 conda-forge
markupsafe 2.0.1 py38h497a2fe_1 conda-forge
matplotlib 3.5.0 py38h578d9bd_0 conda-forge
matplotlib-base 3.5.0 py38hf4fb855_0 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mistune 0.8.4 py38h497a2fe_1005 conda-forge
more-itertools 8.11.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.2 py38h1fd1430_2 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.27 ha770c72_1 conda-forge
mysql-libs 8.0.27 hfa10184_1 conda-forge
natsort 8.0.0 pyhd8ed1ab_0 conda-forge
nbclient 0.5.9 pyhd8ed1ab_0 conda-forge
nbconvert 6.3.0 py38h578d9bd_1 conda-forge
nbformat 5.1.3 pyhd8ed1ab_0 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
nest-asyncio 1.5.1 pyhd8ed1ab_0 conda-forge
networkx 2.6.3 pyhd8ed1ab_1 conda-forge
nodejs 16.12.0 h92b4a50_0 conda-forge
nose 1.3.7 py_1006 conda-forge
notebook 6.4.6 pyha770c72_0 conda-forge
nspr 4.32 h9c3ff4c_1 conda-forge
nss 3.72 hb5efdd6_0 conda-forge
numba 0.53.1 py38h8b71fd7_1 conda-forge
numpy 1.21.4 py38he2449b9_0 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
oniguruma 6.9.7.1 h7f98852_0 conda-forge
openjdk 11.0.1 h516909a_1016 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 1.1.1l h7f98852_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.2.5 py38h1abd341_0 conda-forge
pandoc 2.16.2 h7f98852_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
pango 1.48.10 h54213e6_2 conda-forge
parso 0.8.2 pyhd8ed1ab_0 conda-forge
patsy 0.5.2 pyhd8ed1ab_0 conda-forge
pbzip2 1.1.13 0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.37 h032f7d1_0 conda-forge
perl 5.26.2 h36c2ea0_1008 conda-forge
perl-archive-tar 2.18 pl526_3 bioconda
perl-carp 1.38 pl526_3 bioconda
perl-common-sense 3.74 pl526_2 bioconda
perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda
perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda
perl-exporter 5.72 pl526_1 bioconda
perl-exporter-tiny 1.002001 pl526_0 bioconda
perl-extutils-makemaker 7.36 pl526_1 bioconda
perl-io-compress 2.087 pl526he1b5a44_0 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-json 4.02 pl526_0 bioconda
perl-json-xs 2.34 pl526h6bb024c_3 bioconda
perl-list-moreutils 0.413 1 bioconda
perl-pathtools 3.75 pl526h14c3975_1 bioconda
perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda
perl-threaded 5.26.0 0 bioconda
perl-types-serialiser 1.0 pl526_2 bioconda
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pigz 2.6 h27826a3_0 conda-forge
pillow 8.4.0 py38h8e6f84c_0 conda-forge
pip 21.3.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pluggy 1.0.0 py38h578d9bd_2 conda-forge
prometheus_client 0.12.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.22 pyha770c72_0 conda-forge
psutil 5.8.0 py38h497a2fe_2 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
py 1.11.0 pyh6c4a22f_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.10.0 pyhd8ed1ab_0 conda-forge
pynndescent 0.5.5 pyh6c4a22f_0 conda-forge
pyopenssl 21.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.6 pyhd8ed1ab_0 conda-forge
pyqt 5.12.3 py38h578d9bd_8 conda-forge
pyqt-impl 5.12.3 py38h0ffb2e6_8 conda-forge
pyqt5-sip 4.19.18 py38h709712a_8 conda-forge
pyqtchart 5.12 py38h7400c14_8 conda-forge
pyqtwebengine 5.12.1 py38h7400c14_8 conda-forge
pyrsistent 0.18.0 py38h497a2fe_0 conda-forge
pysocks 1.7.1 py38h578d9bd_4 conda-forge
pytest 6.2.5 py38h578d9bd_1 conda-forge
python 3.8.12 hb7a2778_2_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-isal 0.11.1 py38h497a2fe_1 conda-forge
python_abi 3.8 2_cp38 conda-forge
pytz 2021.3 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py38h497a2fe_3 conda-forge
pyzmq 22.3.0 py38h2035c66_1 conda-forge
q2-alignment 2021.11.0 py38_0 qiime2/label/r2021.11
q2-composition 2021.11.0 py38_0 qiime2/label/r2021.11
q2-cutadapt 2021.11.0 py38_0 qiime2/label/r2021.11
q2-dada2 2021.11.0 py38_0 qiime2/label/r2021.11
q2-deblur 2021.11.0 py38_0 qiime2/label/r2021.11
q2-demux 2021.11.0 py38_0 qiime2/label/r2021.11
q2-diversity 2021.11.0 py38_0 qiime2/label/r2021.11
q2-diversity-lib 2021.11.0 py38_0 qiime2/label/r2021.11
q2-emperor 2021.11.0 py38_0 qiime2/label/r2021.11
q2-feature-classifier 2021.11.0 py38_0 qiime2/label/r2021.11
q2-feature-table 2021.11.0 py38_0 qiime2/label/r2021.11
q2-fragment-insertion 2021.11.0 py38_0 qiime2/label/r2021.11
q2-gneiss 2021.11.0 py38_0 qiime2/label/r2021.11
q2-longitudinal 2021.11.0 py38_0 qiime2/label/r2021.11
q2-metadata 2021.11.0 py38_0 qiime2/label/r2021.11
q2-mystery-stew 2021.11.0 py38_0 qiime2/label/r2021.11
q2-phylogeny 2021.11.0 py38_0 qiime2/label/r2021.11
q2-quality-control 2021.11.0 py38_0 qiime2/label/r2021.11
q2-quality-filter 2021.11.0 py38_0 qiime2/label/r2021.11
q2-sample-classifier 2021.11.0 py38_0 qiime2/label/r2021.11
q2-taxa 2021.11.0 py38_0 qiime2/label/r2021.11
q2-types 2021.11.0 py38_0 qiime2/label/r2021.11
q2-vsearch 2021.11.0 py38_0 qiime2/label/r2021.11
q2cli 2021.11.0 py38_0 qiime2/label/r2021.11
q2galaxy 2021.11.0 py38_0 qiime2/label/r2021.11
q2templates 2021.11.0 py38_0 qiime2/label/r2021.11
qiime2 2021.11.0 py38_0 qiime2/label/r2021.11
qt 5.12.9 hda022c4_4 conda-forge
r-assertthat 0.2.1 r40hc72bb7e_2 conda-forge
r-backports 1.3.0 r40hcfec24a_0 conda-forge
r-base 4.0.5 hb93adac_3 conda-forge
r-bh 1.75.0_0 r40hc72bb7e_0 conda-forge
r-bitops 1.0_7 r40hcfec24a_0 conda-forge
r-brio 1.1.2 r40hcfec24a_0 conda-forge
r-callr 3.7.0 r40hc72bb7e_0 conda-forge
r-cli 3.1.0 r40h03ef668_0 conda-forge
r-cluster 2.1.2 r40h859d828_0 conda-forge
r-colorspace 2.0_2 r40hcfec24a_0 conda-forge
r-crayon 1.4.2 r40hc72bb7e_0 conda-forge
r-desc 1.4.0 r40hc72bb7e_0 conda-forge
r-diffobj 0.3.5 r40hcfec24a_0 conda-forge
r-digest 0.6.28 r40h03ef668_0 conda-forge
r-ellipsis 0.3.2 r40hcfec24a_0 conda-forge
r-evaluate 0.14 r40hc72bb7e_2 conda-forge
r-fansi 0.5.0 r40hcfec24a_0 conda-forge
r-farver 2.1.0 r40h03ef668_0 conda-forge
r-formatr 1.11 r40hc72bb7e_0 conda-forge
r-futile.logger 1.4.3 r40hc72bb7e_1003 conda-forge
r-futile.options 1.0.1 r40hc72bb7e_1002 conda-forge
r-ggplot2 3.3.5 r40hc72bb7e_0 conda-forge
r-glue 1.5.0 r40hcfec24a_0 conda-forge
r-gtable 0.3.0 r40hc72bb7e_3 conda-forge
r-hwriter 1.3.2 r40hc72bb7e_1003 conda-forge
r-isoband 0.2.5 r40h03ef668_0 conda-forge
r-jpeg 0.1_9 r40hcfec24a_0 conda-forge
r-jsonlite 1.7.2 r40hcfec24a_0 conda-forge
r-labeling 0.4.2 r40hc72bb7e_0 conda-forge
r-lambda.r 1.2.4 r40hc72bb7e_1 conda-forge
r-lattice 0.20_45 r40hcfec24a_0 conda-forge
r-latticeextra 0.6_29 r40hc72bb7e_1 conda-forge
r-lifecycle 1.0.1 r40hc72bb7e_0 conda-forge
r-magrittr 2.0.1 r40hcfec24a_1 conda-forge
r-mass 7.3_54 r40hcfec24a_0 conda-forge
r-matrix 1.3_2 r40he454529_0 conda-forge
r-matrixstats 0.61.0 r40hcfec24a_0 conda-forge
r-mgcv 1.8_38 r40he454529_0 conda-forge
r-munsell 0.5.0 r40hc72bb7e_1003 conda-forge
r-nlme 3.1_153 r40h859d828_0 conda-forge
r-permute 0.9_5 r40h785f33e_3 conda-forge
r-pillar 1.6.4 r40hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r40hc72bb7e_1 conda-forge
r-pkgload 1.2.3 r40h03ef668_0 conda-forge
r-plyr 1.8.6 r40h03ef668_1 conda-forge
r-png 0.1_7 r40hcfec24a_1004 conda-forge
r-praise 1.0.0 r40hc72bb7e_1004 conda-forge
r-processx 3.5.2 r40hcfec24a_0 conda-forge
r-ps 1.6.0 r40hcfec24a_0 conda-forge
r-r6 2.5.1 r40hc72bb7e_0 conda-forge
r-rcolorbrewer 1.1_2 r40h785f33e_1003 conda-forge
r-rcpp 1.0.7 r40h03ef668_0 conda-forge
r-rcppparallel 5.1.4 r40h03ef668_0 conda-forge
r-rcurl 1.98_1.5 r40hcfec24a_0 conda-forge
r-rematch2 2.1.2 r40hc72bb7e_1 conda-forge
r-reshape2 1.4.4 r40h03ef668_1 conda-forge
r-rlang 0.4.12 r40hcfec24a_0 conda-forge
r-rprojroot 2.0.2 r40hc72bb7e_0 conda-forge
r-rstudioapi 0.13 r40hc72bb7e_0 conda-forge
r-scales 1.1.1 r40hc72bb7e_0 conda-forge
r-snow 0.4_4 r40hc72bb7e_0 conda-forge
r-stringi 1.7.5 r40hcabe038_0 conda-forge
r-stringr 1.4.0 r40hc72bb7e_2 conda-forge
r-testthat 3.1.0 r40h03ef668_0 conda-forge
r-tibble 3.1.6 r40hcfec24a_0 conda-forge
r-utf8 1.2.2 r40hcfec24a_0 conda-forge
r-vctrs 0.3.8 r40hcfec24a_1 conda-forge
r-vegan 2.5_7 r40h52d45c5_0 conda-forge
r-viridislite 0.4.0 r40hc72bb7e_0 conda-forge
r-waldo 0.3.1 r40hc72bb7e_0 conda-forge
r-withr 2.4.2 r40hc72bb7e_0 conda-forge
raxml 8.2.12 h779adbc_3 bioconda
readline 8.1 h46c0cb4_0 conda-forge
requests 2.25.1 pyhd3deb0d_0 conda-forge
samtools 1.14 hb421002_0 bioconda
scikit-bio 0.5.6 py38h0b5ebd8_4 conda-forge
scikit-learn 0.24.1 py38h658cfdd_0 conda-forge
scipy 1.7.2 py38h56a6a73_0 conda-forge
seaborn 0.11.2 hd8ed1ab_0 conda-forge
seaborn-base 0.11.2 pyhd8ed1ab_0 conda-forge
sed 4.8 he412f7d_0 conda-forge
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
sepp 4.3.10 py38h3252c3a_2 bioconda
setuptools 59.2.0 py38h578d9bd_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sortmerna 2.0 he860b03_4 bioconda
sqlite 3.36.0 h9cd32fc_2 conda-forge
statsmodels 0.13.1 py38h6c62de6_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tbb 2020.2 h4bd325d_4 conda-forge
terminado 0.12.1 py38h578d9bd_1 conda-forge
testpath 0.5.0 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.0.0 pyh8a188c0_0 conda-forge
tk 8.6.11 h27826a3_1 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tornado 6.1 py38h497a2fe_2 conda-forge
tqdm 4.62.3 pyhd8ed1ab_0 conda-forge
traitlets 5.1.1 pyhd8ed1ab_0 conda-forge
typing_extensions 4.0.0 pyha770c72_0 conda-forge
tzlocal 2.1 pyh9f0ad1d_0 conda-forge
umap-learn 0.5.2 py38h578d9bd_0 conda-forge
unicodedata2 13.0.0.post2 py38h497a2fe_4 conda-forge
unifrac 0.20.2 py38hc37a69a_1 bioconda
urllib3 1.26.7 pyhd8ed1ab_0 conda-forge
vsearch 2.7.0 1 bioconda
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.37.0 pyhd8ed1ab_1 conda-forge
widgetsnbextension 3.5.2 py38h578d9bd_1 conda-forge
xmltodict 0.12.0 py_0 conda-forge
xopen 1.2.1 py38h578d9bd_1 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h516909a_0 conda-forge
yq 2.12.2 pyhd8ed1ab_0 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zipp 3.6.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.5.0 ha95c52a_0 conda-forge

(qiime2-2021.11) [email protected]:~$ which ipython
/home/maurice/.local/bin/ipython.

Does this indicate that ipython is coiming for the wrong place?

Thank you for your assistance.

1 Like

@Maurice_Barrett,

Yes, it looks like ipython is coming from a local install rather than your conda environment. Most likely this location is coming before your conda path in your system path($PATH). Fixing this will be specific to your system. From your command line it looks like you are on a linux machine, in which case, you might have a sys admin who should be able to help you resolve this(and may be the one who has to do it for you, depending on how the permissions are set up). The good news is that your QIIME2 install and conda environment look good!

If this is your personal machine, you will have to fix it yourself. You could view your current path with echo $PATH. The path is reset every time your terminal starts up, with its configuration coming from a file(most likely called .bashrc or .zshrc depending on your terminal and stored in your home directory). Here is a general guide to setting your path and here are some conda docs related to getting your path setup. You generally want conda to set its path itself with conda init rather than setting this manually. However, you may end up needing to make changes to the other ipython install using information from the first link.

It is worth noting that the path is read left to right, meaning that the command will be run from the first place that it is found in your path starting from the beginning. I wish I had more specific advice that I could give you, but since this seems to be a system configuration issue(rather than a QIIME 2 specific issue), it is hard be more specific advice at this point. Hopefully I have given you enough here to get you headed in the right direction; feel free to comment again here with any other questions you might have or other issues that you run into :slightly_smiling_face:

2 Likes

Hi @Keegan-Evans

Yes, I think you are very much correct. I can call ipython specifically using directly with /home/maurice/anaconda3/bin and import qiime. You are correct, I am using Linux (ubuntu) and it is my own.

Thanks for your help. I will look at the links you have provide and consider changing my paths variables.

Thanks for the assistance, greatly appreciated. I am running the qiime2 Artifact API just fine now.

2 Likes

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.