Error installing qiime2-2021.8

User Support
1

Hello! I was just trying to install qiime2-2021.8 or qiime2-2022.8 using miniconda, the installation seemed to be successful, however, I received this error message when activated the env.

qiime --help
bash qiime: command not found...

In my conda env, all the packages have been installed

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             5.1                       1_gnu  
bibtexparser              1.3.0              pyhd8ed1ab_0    conda-forge
blas                      1.0                         mkl  
bottleneck                1.3.5            py38h7deecbd_0  
ca-certificates           2022.9.14            ha878542_0    conda-forge
certifi                   2022.9.14          pyhd8ed1ab_0    conda-forge
decorator                 4.4.2                      py_0    conda-forge
dill                      0.3.5.1            pyhd8ed1ab_0    conda-forge
intel-openmp              2021.4.0          h06a4308_3561  
ld_impl_linux-64          2.38                 h1181459_1  
libffi                    3.3                  he6710b0_2  
libgcc-ng                 11.2.0               h1234567_1  
libgomp                   11.2.0               h1234567_1  
libstdcxx-ng              11.2.0               h1234567_1  
mkl                       2021.4.0           h06a4308_640  
mkl-service               2.4.0            py38h95df7f1_0    conda-forge
mkl_fft                   1.3.1            py38h8666266_1    conda-forge
mkl_random                1.2.2            py38h1abd341_0    conda-forge
ncurses                   6.3                  h5eee18b_3  
networkx                  2.8.6              pyhd8ed1ab_0    conda-forge
numexpr                   2.8.3            py38h807cd23_0  
numpy                     1.23.1           py38h6c91a56_0  
numpy-base                1.23.1           py38ha15fc14_0  
openssl                   1.1.1q               h7f8727e_0  
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.3            py38h6a678d5_0  
pip                       22.1.2           py38h06a4308_0  
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
python                    3.8.13               h12debd9_0  
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      2_cp38    conda-forge
pytz                      2022.2.1           pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py38h0a891b7_4    conda-forge
qiime2                    2021.8.0         py38h5479fe0_0    qiime2/label/r2021.8
readline                  8.1.2                h7f8727e_1  
setuptools                63.4.1           py38h06a4308_0  
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.39.2               h5082296_0  
tk                        8.6.12               h1ccaba5_0  
tzlocal                   2.1                pyh9f0ad1d_0    conda-forge
wheel                     0.37.1             pyhd3eb1b0_0  
xz                        5.2.5                h7f8727e_1  
yaml                      0.2.5                h7f98852_2    conda-forge
zlib                      1.2.12               h5eee18b_3

Does anybody know how to solve it?

Thank you so much.

3

Hello @wqrao, it looks like you have QIIME 2 2021.8.0 in that environment but are missing most of the other dependencies which is very strange. If you're ok with QIIME 2 2022.8, can you remove the conda environment you created there then follow the instructions here to install 2022.8 and tell us whether that works or not?

1 Like
4

Hi @Oddant1 !
Thanks for your help. I removed the conda env and created a new one. I used this code to install

conda install -c "qiime2/label/r2022.8" qiime2 -n qiime2-2022.8

when I activated the new env, the same error appeared again. These are the packages in the new env.

# packages in environment at /public/miniconda3/envs/qiime2-2022.8:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
atpublic                  3.0.1              pyhd8ed1ab_0    conda-forge
bibtexparser              1.3.0              pyhd8ed1ab_0    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2022.9.14            ha878542_0    conda-forge
decorator                 4.4.2                      py_0    conda-forge
dill                      0.3.5.1            pyhd8ed1ab_0    conda-forge
flufl.lock                7.1                pyhd8ed1ab_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgfortran-ng            12.1.0              h69a702a_16    conda-forge
libgfortran5              12.1.0              hdcd56e2_16    conda-forge
libgomp                   12.1.0              h8d9b700_16    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libsqlite                 3.39.3               h753d276_0    conda-forge
libstdcxx-ng              12.1.0              ha89aaad_16    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libzlib                   1.2.12               h166bdaf_3    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
networkx                  2.8.6              pyhd8ed1ab_0    conda-forge
numpy                     1.23.3           py38h3a7f9d9_0    conda-forge
openssl                   3.0.5                h166bdaf_2    conda-forge
pandas                    1.5.0            py38h8f669ce_0    conda-forge
pip                       22.2.2             pyhd8ed1ab_0    conda-forge
psutil                    5.9.2            py38h0a891b7_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
python                    3.8.13          ha86cf86_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      2_cp38    conda-forge
pytz                      2022.2.1           pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py38h0a891b7_4    conda-forge
qiime2                    2022.8.3                 py38_0    qiime2/label/r2022.8
readline                  8.1.2                h0f457ee_0    conda-forge
setuptools                65.3.0             pyhd8ed1ab_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.39.3               h4ff8645_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tzlocal                   2.1                pyh9f0ad1d_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge

I can't follow the tutorial in qiime2.org to install it because our server doesn't have access to GitHub.

5

@wqrao, you don't need access to github to create a QIIME 2 conda environment. These are the commands in the tutorial that you need to run.

Download the file and create an environment from it

wget https://data.qiime2.org/distro/core/qiime2-2022.8-py38-linux-conda.yml
conda env create -n qiime2-2022.8 --file qiime2-2022.8-py38-linux-conda.yml

And this if you want to clean up the environment file

rm qiime2-2022.8-py38-linux-conda.yml
6

Thanks! I have installed it successfully.

8

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