Qiime2 not Working

I was able to download Qiime2 using the tutorial. However the command line tutorial is not working for me. For everything in that tutorial I keep getting “command not found”. Not even source tab-qiime works. Please let me know what I can do to fix this. Thanks.

Hi @Stephanieorch! Sorry to hear things aren’t working well for you :frowning: , but we need a bit more information from you in order to help:

  1. What version of QIIME 2 did you install?
  2. Did you follow the official Native install directions, or are you using one of the Virtual machine builds?
  3. If you performed the native install, did you follow the activation step? This needs to happen every time you start a new QIIME 2 session.
  4. What was the exact command you were running? Please copy and paste.
  5. What is the complete error you are seeing when running the command in 4.? Please copy and paste.

Thanks!! :t_rex:

  1. I installed QIIME2 in the conda environment for mac OS/OSX.
  2. I follow the native install directions.
  3. Yes I followed the activation step.
  4. I attempted to run qiime, then I tried qiime info, then I tried source tab-qiime. None of these 3 worked.
  5. For running qiime and qiime info I get this: -bash: qiime: command not found
    For running source tab-qiime I get this: -bash: tab-qiime: No such file or directory

@Stephanieorch - thanks so much for the detailed followup!

It sounds like something funky is happening with your conda setup, here are some things you can run, and provide us with the output from, to help track this down.

  1. Fire up a new terminal, and before activating your environment, run conda env list; copy-and-paste the command and results here. An example of what you might see:
$ conda env list
# conda environments:
q2dev-2017.8             /Users/matthew/miniconda3/envs/q2dev-2017.8
q2dev-2017.9             /Users/matthew/miniconda3/envs/q2dev-2017.9
qiime2-2017.8            /Users/matthew/miniconda3/envs/qiime2-2017.8
qiime2-2017.9            /Users/matthew/miniconda3/envs/qiime2-2017.9
workshop-prov            /Users/matthew/miniconda3/envs/workshop-prov
root                  *  /Users/matthew/miniconda3
  1. Next, run source activate qiime2-2017.9, and once it is activated, run conda list; copy-and-paste the command and results here. An example of what you might see:
$ source activate qiime2-2017.9
(qiime2-2017.9) $ conda list
# packages in environment at /Users/matthew/miniconda3/envs/qiime2-2017.9:
appnope                   0.1.0                    py35_0    conda-forge
asn1crypto                0.22.0                   py35_0    conda-forge
bioconductor-biobase      2.34.0                 r3.3.2_0    bioconda
bioconductor-biocgenerics 0.22.0                 r3.3.2_0    bioconda
bioconductor-biocparallel 1.6.6                  r3.3.2_1    bioconda
bioconductor-biostrings   2.42.1                 r3.3.2_0    bioconda
bioconductor-dada2        1.4.0                  r3.3.2_0    bioconda
bioconductor-genomeinfodb 1.10.3                 r3.3.2_0    bioconda
bioconductor-genomicalignments 1.10.0                 r3.3.2_0    bioconda
bioconductor-genomicranges 1.26.4                 r3.3.2_0    bioconda
bioconductor-iranges      2.8.2                  r3.3.2_0    bioconda
bioconductor-rsamtools    1.26.1                 r3.3.2_0    bioconda
bioconductor-s4vectors    0.12.2                 r3.3.2_0    bioconda
bioconductor-shortread    1.32.0                 r3.3.2_0    bioconda
bioconductor-summarizedexperiment 1.4.0                  r3.3.2_2    bioconda
bioconductor-xvector      0.14.1                 r3.3.2_0    bioconda
bioconductor-zlibbioc     1.20.0                 r3.3.2_1    bioconda
biom-format               2.1.5                    py35_3    qiime2
blast                     2.6.0               boost1.64_2    bioconda
bleach                    2.0.0                    py35_0    conda-forge
bokeh                     0.12.9                   py35_0    conda-forge
ca-certificates           2017.7.27.1                   0    conda-forge
cachecontrol              0.12.3                   py35_0
cairo                     1.14.6                        4    conda-forge
certifi                   2017.7.27.1              py35_0    conda-forge
cffi                      1.10.0                   py35_0    conda-forge
chardet                   3.0.4                    py35_0    conda-forge
click                     6.7                      py35_0    conda-forge
cryptography              2.0.3                    py35_0    conda-forge
curl                      7.54.1                        0    conda-forge
cycler                    0.10.0                   py35_0    conda-forge
cython                    0.27                     py35_0    conda-forge
deblur                    1.0.2                    py35_0    biocore
decorator                 4.1.2                    py35_0    conda-forge
emperor                   1.0.0beta11              py35_2    conda-forge
entrypoints               0.2.3                    py35_1    conda-forge
fastcluster               1.1.23              np113py35_0    conda-forge
fasttree                  2.1.9                         2    bioconda
fontconfig                2.12.1                        4    conda-forge
freetype                  2.7                           1    conda-forge
future                    0.16.0                   py35_0    conda-forge
gettext                               0    conda-forge
glib                      2.51.4                        0    conda-forge
gneiss                    0.4.1            py35ha7bfd4e_6    biocore
graphite2                 1.3.9                         0    conda-forge
gsl                       2.1                           2    conda-forge
h5py                      2.7.0               np113py35_0
harfbuzz                  1.4.3                         0    conda-forge
hdf5                      1.8.17                       11    conda-forge
html5lib                  0.999999999              py35_0    conda-forge
icu                       58.1                          1    conda-forge
idna                      2.6                        py_0    conda-forge
ijson                     2.3                      py35_0    qiime2
intel-openmp              2018.0.0             hdd0ccc9_7    https://repo.continuum.io/pkgs/main
ipykernel                 4.6.1                    py35_0    conda-forge
ipython                   6.2.0                    py35_0    conda-forge
ipython_genutils          0.2.0                    py35_0    conda-forge
ipywidgets                7.0.1                      py_2    conda-forge
jedi                      0.10.2                   py35_0    conda-forge
jinja2                    2.9.6                    py35_0    conda-forge
jpeg                      9b                            1    conda-forge
jsonschema                2.6.0                    py35_0    conda-forge
jupyter_client            5.1.0                    py35_0    conda-forge
jupyter_core              4.3.0                    py35_0    conda-forge
krb5                      1.14.2                        0    conda-forge
libcxx                    4.0.1                h579ed51_0    https://repo.continuum.io/pkgs/main
libcxxabi                 4.0.1                hebd6815_0    https://repo.continuum.io/pkgs/main
libffi                    3.2.1                         3    conda-forge
libgcc                    4.8.5               hdbeacc1_10    https://repo.continuum.io/pkgs/main
libgfortran               3.0.1                h93005f0_2    https://repo.continuum.io/pkgs/main
libiconv                  1.14                          4    conda-forge
libpng                    1.6.28                        1    conda-forge
libsodium                 1.0.10                        0    conda-forge
libssh2                   1.8.0                         1    conda-forge
libtiff                   4.0.7                         0    conda-forge
libxml2                   2.9.5                         0    conda-forge
lockfile                  0.12.2                   py35_0    conda-forge
mafft                     7.221                         0    bioconda
markupsafe                1.0                      py35_0    conda-forge
matplotlib                2.0.2                    py35_2    conda-forge
mistune                   0.7.4                    py35_0    conda-forge
mkl                       2018.0.0             hc285769_4    https://repo.continuum.io/pkgs/main
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                  5.1.0                    py35_0    conda-forge
numpy                     1.13.1           py35he58e7f4_2    https://repo.continuum.io/pkgs/main
openssl                   1.0.2l                        0    conda-forge
pandas                    0.20.3                   py35_1    conda-forge
pandoc                    1.19.2                        0    conda-forge
pandocfilters             1.4.1                    py35_0    conda-forge
pango                     1.40.4                        0    conda-forge
patsy                     0.4.1                    py35_0    conda-forge
pcre                      8.39                          0    conda-forge
pexpect                   4.2.1                    py35_0    conda-forge
pickleshare               0.7.4                    py35_0    conda-forge
pip                       9.0.1                    py35_0    conda-forge
pixman                    0.34.0                        0    conda-forge
prompt_toolkit            1.0.15                   py35_0    conda-forge
psutil                    5.2.2                    py35_0    conda-forge
ptyprocess                0.5.2                    py35_0    conda-forge
py                        1.4.34                   py35_0
pycparser                 2.18                     py35_0    conda-forge
pygments                  2.2.0                    py35_0    conda-forge
pyopenssl                 17.2.0                   py35_0    conda-forge
pyparsing                 2.2.0                    py35_0    conda-forge
pysocks                   1.6.7                    py35_0    conda-forge
pytest                    3.2.1                    py35_0
python                    3.5.4                         0    conda-forge
python-dateutil           2.6.1                    py35_0    conda-forge
pytz                      2017.2                   py35_0    conda-forge
pyyaml                    3.12                     py35_1    conda-forge
pyzmq                     16.0.2                   py35_2    conda-forge
q2-alignment              2017.9.0                 py35_0    qiime2/label/r2017.9
q2-composition            2017.9.0                 py35_0    qiime2/label/r2017.9
q2-dada2                  2017.9.0                 py35_0    qiime2/label/r2017.9
q2-deblur                 2017.9.0                 py35_0    qiime2/label/r2017.9
q2-demux                  2017.9.0                 py35_0    qiime2/label/r2017.9
q2-diversity              2017.9.0                 py35_0    qiime2/label/r2017.9
q2-emperor                2017.9.0                 py35_0    qiime2/label/r2017.9
q2-feature-classifier     2017.9.0                 py35_0    qiime2/label/r2017.9
q2-feature-table          2017.9.0                 py35_0    qiime2/label/r2017.9
q2-gneiss                 2017.9.0                 py35_0    qiime2/label/r2017.9
q2-longitudinal           2017.9.0                 py35_0    qiime2/label/r2017.9
q2-metadata               2017.9.0                 py35_0    qiime2/label/r2017.9
q2-phylogeny              2017.9.0                 py35_0    qiime2/label/r2017.9
q2-quality-filter         2017.9.0                 py35_0    qiime2/label/r2017.9
q2-sample-classifier      2017.9.0                 py35_0    qiime2/label/r2017.9
q2-taxa                   2017.9.0                 py35_0    qiime2/label/r2017.9
q2-types                  2017.9.0                 py35_0    qiime2/label/r2017.9
q2-vsearch                2017.9.0                 py35_0    qiime2/label/r2017.9
q2cli                     2017.9.0                 py35_0    qiime2/label/r2017.9
q2templates               2017.9.0                 py35_0    qiime2/label/r2017.9
qiime2                    2017.9.0                 py35_0    qiime2/label/r2017.9
r-base                    3.3.2                         5    conda-forge
r-bh                      1.62.0_1               r3.3.2_0    conda-forge
r-bitops                  1.0_6                  r3.3.2_0    conda-forge
r-colorspace              1.3_2                  r3.3.2_0    conda-forge
r-data.table              1.10.4                 r3.3.2_0    conda-forge
r-dichromat               2.0_0                  r3.3.2_0    conda-forge
r-digest                  0.6.12                 r3.3.2_0    conda-forge
r-futile.logger           1.4.3                  r3.3.2_0    conda-forge
r-futile.options          1.0.0                  r3.3.2_0    conda-forge
r-ggplot2                 2.2.1                  r3.3.2_0    conda-forge
r-gtable                  0.2.0                  r3.3.2_0    conda-forge
r-hwriter                 1.3.2                  r3.3.2_0    conda-forge
r-labeling                0.3                    r3.3.2_0    conda-forge
r-lambda.r                1.1.9                  r3.3.2_0    conda-forge
r-lattice                 0.20_34                r3.3.2_0    conda-forge
r-latticeextra            0.6_28                 r3.3.2_0    conda-forge
r-lazyeval                0.2.0                  r3.3.2_0    conda-forge
r-magrittr                1.5                    r3.3.2_0    conda-forge
r-mass                    7.3_45                 r3.3.2_0    conda-forge
r-matrix                  1.2_7.1                r3.3.2_0    conda-forge
r-munsell                 0.4.3                  r3.3.2_0    conda-forge
r-plyr                    1.8.4                  r3.3.2_0    conda-forge
r-rcolorbrewer            1.1_2                  r3.3.2_0    conda-forge
r-rcpp                    0.12.10                r3.3.2_0    conda-forge
r-rcppparallel            4.3.20                 r3.3.2_0    conda-forge
r-rcurl                   1.95_4.8               r3.3.2_0    conda-forge
r-reshape2                1.4.2                  r3.3.2_0    conda-forge
r-rlang                   0.1.2                  r3.3.2_0    conda-forge
r-scales                  0.4.1                  r3.3.2_0    conda-forge
r-snow                    0.4_2                  r3.3.2_0    conda-forge
r-stringi                 1.1.2                  r3.3.2_0    conda-forge
r-stringr                 1.2.0                  r3.3.2_0    conda-forge
r-tibble                  1.3.3                  r3.3.2_0    conda-forge
readline                  6.2                           0    conda-forge
requests                  2.18.4                   py35_1    conda-forge
scikit-bio                0.5.1               np113py35_0
scikit-learn              0.19.0           py35hd036984_2    https://repo.continuum.io/pkgs/main
scipy                     0.19.1           py35hf362045_3    https://repo.continuum.io/pkgs/main
seaborn                   0.8.1                    py35_0    conda-forge
setuptools                36.3.0                   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                 0.6                      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                   2.0.3                         1    bioconda
wcwidth                   0.1.7                    py35_0    conda-forge
webencodings              0.5                      py35_0    conda-forge
wheel                     0.30.0                     py_1    conda-forge
widgetsnbextension        3.0.3                    py35_2    conda-forge
xz                        5.2.3                         0    conda-forge
yaml                      0.1.6                         0    conda-forge
zeromq                    4.2.1                         1    conda-forge
zlib                      1.2.8                         3    conda-forge
  1. Next, run which qiime, copy-and-paste the command and results here. An example of what you might see:
(qiime2-2017.9) $ which qiime
  1. Finally, run qiime info; copy-and-paste the command and results here (I know you provided a bit of this earlier, but we want to make sure we have our bases covered). An example of what you might see:
(qiime2-2017.9) $ qiime info
System versions
Python version: 3.5.4
QIIME 2 release: 2017.9
QIIME 2 version: 2017.9.0
q2cli version: 2017.9.0

Installed plugins
alignment 2017.9.0
composition 2017.9.0
dada2 2017.9.0
deblur 2017.9.0
demux 2017.9.0
diversity 2017.9.0
emperor 2017.9.0
feature-classifier 2017.9.0
feature-table 2017.9.0
gneiss 2017.9.0
longitudinal 2017.9.0
metadata 2017.9.0
phylogeny 2017.9.0
quality-filter 2017.9.0
sample-classifier 2017.9.0
taxa 2017.9.0
types 2017.9.0
vsearch 2017.9.0

Application config directory
/Users/matthew/Library/Application Support/q2cli

Getting help
To get help with QIIME 2, visit https://qiime2.org

Citing QIIME 2
If you use QIIME 2 in any published work, you should cite QIIME 2 and the plugins that you used. To display the citations for QIIME 2 and all installed plugins, run:

  qiime info --citations

Thanks! We will get to the bottom of this!

1 Like

I have run each of the commands and it wasn’t very similar to what you got. This is what my commands gave me:

Stephanies-MacBook-Pro:~ stephanieorch$ conda env list
# conda environments:
qiime2-2017.9            /Users/stephanieorch/miniconda3/envs/qiime2-2017.9
root                  *  /Users/stephanieorch/miniconda3

Stephanies-MacBook-Pro:~ stephanieorch$ source activate qiime2-2017.9
(qiime2-2017.9) Stephanies-MacBook-Pro:~ stephanieorch$ which qiime
(qiime2-2017.9) Stephanies-MacBook-Pro:~ stephanieorch$ qiime info
-bash: qiime: command not found

Ah ha! I think we are onto something here! It looks like your installation of QIIME 2 is incomplete — perhaps there was a network interruption, or anaconda.org (the service behind conda) experienced some kind of outage or issue. Either way, we should be able to clean things up by running a few commands, and then you should be able to reinstall QIIME 2 (fingers crossed!).

To clean up:

$ conda env remove -n qiime2-2017.9
$ conda clean -y --all
$ conda update conda

Then, head on over to the docs and follow the installation instructions (just like you did before!), and hopefully things will go better for you this time. Please keep us posted! :balloon:

I’ve tried to upload it multiple times but I keep getting this error:

CondaError: CondaHTTPError: HTTP 403 FORBIDDEN for url https://conda.anaconda.org/conda-forge/osx-64/tk-8.5.19-2.tar.bz2
Elapsed: 00:00.504566

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.


Hi @Stephanieorch - what happens when you click that link above? You should see something like this:

If you don’t, it sounds like there might be some network settings at play here (for example, a firewall, or a roaming/guest account on an institutional wifi network). Unfortunately, there isn’y much we can do to help you with that, if the network is in fact at play here - I would suggest coordinating with your IT help desk then.

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