qiime: command not found

[kas]

Hi,
I installed qiime2-2022.8 using qiime2-2022.8-py38-linux-conda.yml, but for some reason, the qiime command was not found when I tried to use it, therefore I removed the environment and reinstalled it with the following commands:

conda env remove -n qiime2-2022.8
conda clean -y --all
conda update conda
conda env create -n qiime2-2022.8 --file qiime2-2022.8-py38-linux-conda.yml
conda update -n base -c defaults conda
conda activate qiime2-2022.8

Still, when I type:
(qiime2-2022.8) qiime --help
-bash: qiime: command not found

In addition the conda update conda gets back with the following error message... Could this be an issue?

EnvironmentNotWritableError: The current user does not have write permissions to the target environment.
environment location: /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/miniconda3-4.5.4-hivczbzklvoccmuifapprxz7humnmn5c
uid: 44266
gid: 44267

Thanks

[colinbrislawn (Colin J Brislawn)]

Hello Kas,

Welcome to the forums!

Unfortunately, you have already found your issue and I'm not sure we can help...

@kas

EnvironmentNotWritableError: The current user does not have write permissions to the target environment.

I've seen errors like this when an admin installed conda on a supercomputer, so conda was running from the admin's account and normal users (like me) could not always use conda environments like normal.

Are you running conda installed by an admin or another user? If so, installing conda yourself may fix this problem! Or ask your admin

[kas]

Hi Colin,

Thanks for the reply. I need HPC for executing the silva related commands, therefore I am working on the qiime setup on a remote server.

On HPC they have miniconda3-4.5.4 and this cannot be modified/updated so I have to work with this version.

The step where I am stuck

conda env create -n qiime2-2022.2 --file qiime2-2022.2-py38-linux-conda.yml

The error message

Collecting package metadata: done
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:

• bioconductor-zlibbioc=1.40.0
• gneiss=0.4.6
• libclang=14.0.4 -> libclang13==14.0.4=default_h3a83d3e_0 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='14.0.4|14.0.4.*']
• libclang=14.0.4 -> libclang13==14.0.4=default_h3a83d3e_0 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
• matplotlib-base=3.5.2 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> llvmdev[version='13.0.1|13.0.1.*'] -> llvm-tools=13.0.1 -> clang=13.0.1 -> clang-13==13.0.1=default_hc23dcda_0 -> clang-tools==13.0.1 -> clangdev==13.0.1 -> clangxx==13.0.1=default_ha53f305_0
• matplotlib-base=3.5.2 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> llvmdev[version='13.0.1|13.0.1.*'] -> llvm-tools=13.0.1 -> clang=13.0.1 -> clang-13==13.0.1=default_hc23dcda_0 -> clang-tools==13.0.1 -> clangdev==13.0.1 -> libclang-cpp==13.0.1=default_hc23dcda_0
• matplotlib-base=3.5.2 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> llvmdev[version='13.0.1|13.0.1.*'] -> llvm-tools=13.0.1 -> clang=13.0.1 -> clang-13==13.0.1=default_hc23dcda_0 -> clang-tools==13.0.1 -> libclang=13
• matplotlib-base=3.5.2 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> llvmdev[version='13.0.1|13.0.1.*'] -> llvm-tools=13.0.1 -> clang=13.0.1 -> clang-13==13.0.1=default_hc23dcda_0 -> clang-tools==13.0.1 -> llvm=13.0.1
• matplotlib-base=3.5.2 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='>=9.0.1'] -> openmp[version='14.0.4|14.0.4.*']
• matplotlib-base=3.5.2 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] -> openmp_impl==9999
• matplotlib-base=3.5.2 -> pypy3.9[version='>=7.3.9'] -> libffi[version='>=3.4,<4.0a0']
  Use "conda search --info" to see the dependencies for each package.

[colinbrislawn (Colin J Brislawn)]

Let's start here:

@kas

conda env create -n qiime2-2022.2 --file qiime2-2022.2-py38-linux-conda.yml

That's an old version of Qiime2. Is there a reason you are using the February 2022 version?

Have you tried the August 2022 version: Natively installing QIIME 2 — QIIME 2 2022.8.3 documentation

[kas]

Hi Colin,

Yes, I tried the 2022.8 version as well, there my error message is:

conda env create -n qiime2-2022.8 --file qiime2-2022.8-py38-linux-conda.yml
Collecting package metadata: done
Solving environment: failed

ResolvePackageNotFound:

• ipython=8.5.0 -> __win
• ipython=8.5.0 -> __osx
• ipython=8.5.0 -> __linux
• qt-main=5.15.4 -> __glibc[version='>=2.17,<3.0.a0']
• pyqt=5.15.7 -> qt-main[version='>=5.15.6,<5.16.0a0'] -> __glibc[version='>=2.17,<3.0.a0']
• pyqt=5.15.7 -> qt-webengine[version='5.15.*,>=5.15.9,<5.16.0a0']
• libudev1=249 -> __glibc[version='>=2.17,<3.0.a0']

[colinbrislawn (Colin J Brislawn)]

Tell me more about this remote server. Is it Linux, and if so, what flavor/distro? Debian, RHEL?

@kas

On HPC they have miniconda3-4.5.4 and this cannot be modified/updated so I have to work with this version.

If you can't change it, who can? Can you ask the admins to help you get Qiime2 installed, or perhaps you can install Miniconda yourself, in your home directory, so you have your own Conda environment to test.

[kas]

Hi Colin,

Many thanks for the message. I changed from university HPC to azure where I had access to installing and updating conda. It solved the whole problem