# "bash: qiime: command not found..." when conda env has qiime2 installed and is activated
**URL:** https://forum.qiime2.org/t/bash-qiime-command-not-found-when-conda-env-has-qiime2-installed-and-is-activated/30278
**Category:** Technical Support
**Created:** [May 20, 2024, 6:30pm UTC](https://forum.qiime2.org/t/bash-qiime-command-not-found-when-conda-env-has-qiime2-installed-and-is-activated/30278 "2024-05-20T18:30:21Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@airborne\_manatee](https://forum.qiime2.org/u/airborne_manatee)
#### Post date: [May 20, 2024, 6:30pm UTC](https://forum.qiime2.org/t/bash-qiime-command-not-found-when-conda-env-has-qiime2-installed-and-is-activated/30278/1 "2024-05-20T18:30:21Z")
I am receiving the following error when trying to run any qiime commend (eg: qiime --help):
bash: qiime: command not found...
My conda environment is activated and running "conda list" reveals that qiime2 is installed. I've tried uninstalling and reinstalling qiime2, creating fresh conda environments and installing various qiime2 versions into them, creating conda environments from yaml files accessible from various corners of the internet, and have attempted doing all of these things again after updating conda. Every attempt results in the same error. I've also tried doing this on two different college's HPCs that I have access to.
Here are some details about my software versions that may be relevant:
current qiime2 version: 2024.2.0 (I've also tried with 2023.7.0, 2024.2.0, and 2022.11.1)
current conda version: 24.3.0 (I've also tried with 23.3.1)
If I can provide any other information that will help you understand the problem, I'm happy to provide it. Thank you for your help!
---
### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [May 20, 2024, 6:39pm UTC](https://forum.qiime2.org/t/bash-qiime-command-not-found-when-conda-env-has-qiime2-installed-and-is-activated/30278/2 "2024-05-20T18:39:15Z")
Hello @airborne_manatee,
Can you activate your qiime2 environment and run `echo $PATH`, `conda info`, and `conda list` and post the output from each?
---
### Author:  [@airborne\_manatee](https://forum.qiime2.org/u/airborne_manatee)
#### Post date: [May 20, 2024, 6:54pm UTC](https://forum.qiime2.org/t/bash-qiime-command-not-found-when-conda-env-has-qiime2-installed-and-is-activated/30278/3 "2024-05-20T18:54:11Z")
Sure thing!
echo $PATH outputs the following:
/home/gr104/software/miniforge3/envs/cT\_qiime2/bin:/home/gr104/software/miniforge3/condabin:/home/gr104/.local/bin:/home/gr104/bin:/usr/local/mpi/intel/openmpi-cuda12.4-4.1.6/bin:/opt/intel/oneapi/compiler/2024.0/bin:/opt/intel/oneapi/compiler/2024.0/opt/oclfpga/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/cuda/bin
conda info outputs the following:
active environment : cT\_qiime2
active env location : /home/gr104/software/miniforge3/envs/cT\_qiime2
shell level : 1
user config file : /home/gr104/.condarc
populated config files : /home/gr104/software/miniforge3/.condarc
/home/gr104/.condarc
conda version : 24.3.0
conda-build version : not installed
python version : 3.10.14.final.0
solver : libmamba (default)
virtual packages : \_\_archspec=1=sapphirerapids
\_\_conda=24.3.0=0
\_\_glibc=2.34=0
\_\_linux=5.14.0=0
\_\_unix=0=0
base environment : /home/gr104/software/miniforge3 (writable)
conda av data dir : /home/gr104/software/miniforge3/etc/conda
conda av metadata url : None
channel URLs : [conda-forge/linux-64](https://conda.anaconda.org/conda-forge/linux-64)
[conda-forge/noarch](https://conda.anaconda.org/conda-forge/noarch)
package cache : /home/gr104/software/miniforge3/pkgs
/home/gr104/.conda/pkgs
envs directories : /home/gr104/software/miniforge3/envs
/home/gr104/.conda/envs
platform : linux-64
user-agent : conda/24.3.0 requests/2.31.0 CPython/3.10.14 Linux/5.14.0-362.24.1.el9\_3.x86\_64 rocky/9.3 glibc/2.34 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8
UID:GID : 3020:3001
netrc file : None
offline mode : False
conda list outputs the following:
packages in environment at /home/gr104/software/miniforge3/envs/cT\_qiime2:
Name Version Build Channel
\_libgcc\_mutex 0.1 conda\_forge conda-forge
\_openmp\_mutex 4.5 2\_gnu conda-forge
appdirs 1.4.4 pyh9f0ad1d\_0 conda-forge
atpublic 3.0.1 pyhd8ed1ab\_0 conda-forge
bcrypt 4.1.2 py38h0cc4f7c\_0 conda-forge
bibtexparser 1.4.1 pyhd8ed1ab\_0 conda-forge
brotli-python 1.1.0 py38h17151c0\_1 conda-forge
bzip2 1.0.8 hd590300\_5 conda-forge
ca-certificates 2024.2.2 hbcca054\_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab\_0 conda-forge
cffi 1.16.0 py38h6d47a40\_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab\_0 conda-forge
cryptography 42.0.7 py38h1407eca\_0 conda-forge
decorator 4.4.2 py\_0 conda-forge
dill 0.3.8 pyhd8ed1ab\_0 conda-forge
flufl.lock 7.1 pyhd8ed1ab\_0 conda-forge
globus-sdk 3.41.0 pyhd8ed1ab\_0 conda-forge
icu 73.2 h59595ed\_0 conda-forge
idna 3.7 pyhd8ed1ab\_0 conda-forge
importlib\_resources 6.4.0 pyhd8ed1ab\_0 conda-forge
keyutils 1.6.1 h166bdaf\_0 conda-forge
krb5 1.21.2 h659d440\_0 conda-forge
ld\_impl\_linux-64 2.40 h55db66e\_0 conda-forge
libblas 3.9.0 22\_linux64\_openblas conda-forge
libcblas 3.9.0 22\_linux64\_openblas conda-forge
libedit 3.1.20191231 he28a2e2\_2 conda-forge
libffi 3.4.2 h7f98852\_5 conda-forge
libgcc-ng 13.2.0 h77fa898\_7 conda-forge
libgfortran-ng 13.2.0 h69a702a\_7 conda-forge
libgfortran5 13.2.0 hca663fb\_7 conda-forge
libgomp 13.2.0 h77fa898\_7 conda-forge
libiconv 1.17 hd590300\_2 conda-forge
liblapack 3.9.0 22\_linux64\_openblas conda-forge
libnsl 2.0.1 hd590300\_0 conda-forge
libopenblas 0.3.27 pthreads\_h413a1c8\_0 conda-forge
libsodium 1.0.18 h36c2ea0\_1 conda-forge
libsqlite 3.45.3 h2797004\_0 conda-forge
libstdcxx-ng 13.2.0 hc0a3c3a\_7 conda-forge
libuuid 2.38.1 h0b41bf4\_0 conda-forge
libxcrypt 4.4.36 hd590300\_1 conda-forge
libxml2 2.12.7 hc051c1a\_0 conda-forge
libxslt 1.1.39 h76b75d6\_0 conda-forge
libzlib 1.2.13 hd590300\_5 conda-forge
lxml 5.2.2 py38h81c7c4b\_0 conda-forge
ncurses 6.5 h59595ed\_0 conda-forge
networkx 3.1 pyhd8ed1ab\_0 conda-forge
numpy 1.24.4 py38h59b608b\_0 conda-forge
openssl 3.3.0 hd590300\_0 conda-forge
pandas 1.5.3 py38hdc8b05c\_1 conda-forge
paramiko 3.4.0 pyhd8ed1ab\_0 conda-forge
parsl 2023.12.4 pyhd8ed1ab\_0 conda-forge
pip 24.0 pyhd8ed1ab\_0 conda-forge
psutil 5.9.8 py38h01eb140\_0 conda-forge
pycparser 2.22 pyhd8ed1ab\_0 conda-forge
pyjwt 2.8.0 pyhd8ed1ab\_1 conda-forge
pynacl 1.5.0 py38h01eb140\_3 conda-forge
pyparsing 3.1.2 pyhd8ed1ab\_0 conda-forge
pysocks 1.7.1 pyha2e5f31\_6 conda-forge
python 3.8.19 hd12c33a\_0\_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab\_0 conda-forge
python\_abi 3.8 4\_cp38 conda-forge
pytz 2024.1 pyhd8ed1ab\_0 conda-forge
pyyaml 6.0.1 py38h01eb140\_1 conda-forge
pyzmq 26.0.3 py38ha44f8e3\_0 conda-forge
qiime2 2024.2.0 py38h1da1538\_0 qiime2
readline 8.2 h8228510\_1 conda-forge
requests 2.31.0 pyhd8ed1ab\_0 conda-forge
setproctitle 1.3.3 py38h01eb140\_0 conda-forge
setuptools 69.5.1 pyhd8ed1ab\_0 conda-forge
six 1.16.0 pyh6c4a22f\_0 conda-forge
tblib 3.0.0 pyhd8ed1ab\_0 conda-forge
tk 8.6.13 noxft\_h4845f30\_101 conda-forge
tomlkit 0.12.5 pyha770c72\_0 conda-forge
typeguard 2.13.3 pyhd8ed1ab\_0 conda-forge
typing-extensions 4.11.0 hd8ed1ab\_0 conda-forge
typing\_extensions 4.11.0 pyha770c72\_0 conda-forge
tzlocal 2.1 pyh9f0ad1d\_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab\_0 conda-forge
wheel 0.43.0 pyhd8ed1ab\_1 conda-forge
xz 5.2.6 h166bdaf\_0 conda-forge
yaml 0.2.5 h7f98852\_2 conda-forge
zeromq 4.3.5 h75354e8\_4 conda-forge
zipp 3.17.0 pyhd8ed1ab\_0 conda-forge
---
### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [May 20, 2024, 7:06pm UTC](https://forum.qiime2.org/t/bash-qiime-command-not-found-when-conda-env-has-qiime2-installed-and-is-activated/30278/4 "2024-05-20T19:06:51Z")
Hello @airborne_manatee,
You have qiime2 installed but no other qiime2-related packages. Importantly, you don't have `q2cli` which is needed for `qiime` to work on your command line.
Do you want a more minimal installation of qiime than those recommended in the [installation documentation](https://docs.qiime2.org/2024.2/install/native/)? If so, then you can just install `q2cli` with
> `conda install q2cli -c https://packages.qiime2.org/qiime2/2024.2/tiny/released`
If not, then just follow the linked-to instructions. Hope this helps.
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### Author:  [@airborne\_manatee](https://forum.qiime2.org/u/airborne_manatee)
#### Post date: [May 20, 2024, 8:40pm UTC](https://forum.qiime2.org/t/bash-qiime-command-not-found-when-conda-env-has-qiime2-installed-and-is-activated/30278/5 "2024-05-20T20:40:49Z")
That solved the issue. Thank you for your help!
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [June 21, 2024, 2:41am UTC](https://forum.qiime2.org/t/bash-qiime-command-not-found-when-conda-env-has-qiime2-installed-and-is-activated/30278/6 "2024-06-21T02:41:47Z")
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