GM, first time poster here. I'm trying to help a user in our environment get QIIME2 working.
The user is on a windows 10 machine but we have WSL installed and are using Ubuntu2 as the distro. I'm using the instructions posted here:
Natively installing QIIME 2 — QIIME 2 2023.9.2 documentation
I've got Conda and Mamba installed but cannot create the environment using "mamba env create" command.
- Have you searched for the problem on the forum? It is rare that we see a new question asked, so make sure you do your homework before asking for us to commit our time to helping you.
Yes, there are many entries for my issue but I'm not seeing a specific one with my issue being resolved.
- Version of QIIME 2 you are running, and how it is installed (e.g. Virtualbox, conda, etc.)
Haven't gotten the QIIME2 installation working yet.
- What is the exact command or commands you ran? Copy and paste please.
1 - wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2023.9-py38-linux-conda.yml
2 - mamba env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml
I am unable to download the file using command "1" but was able to download it using the no check certificate flag. I then tried to use command "2" but received another error.
- What is the exact error message? If you didn't run the command with the --verbose flag, please re-run and copy-and-paste the results.
-------------------------------------------------------1--------------------------------------------------------------------------------
--2023-11-08 17:08:57-- https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2023.9-py38-linux-conda.yml
Resolving data.qiime2.org (data.qiime2.org)... 54.200.1.12
Connecting to data.qiime2.org (data.qiime2.org)|54.200.1.12|:443... connected.
ERROR: cannot verify data.qiime2.org's certificate, issued by ‘[email protected],CN=A10_RES2_SSLi_Cert,OU=ESN,O=Department of the Interior,L=Reston,ST=VA,C=US’:
Unable to locally verify the issuer's authority.
To connect to data.qiime2.org insecurely, use `--no-check-certificate'.
---------------------------------------------------2------------------------------------------------------------------------------------Retrieving notices: ...working... done
https://packages.qiime2.org/qiime2/2023.9/amplic.. Checked 6.4s
https://packages.qiime2.org/qiime2/2023.9/amplic.. Checked 6.0s
conda-forge/noarch 12.5MB @ 10.0MB/s 1.2s
pkgs/r/linux-64 No change
pkgs/main/noarch No change
bioconda/noarch 4.7MB @ 3.5MB/s 1.3s
bioconda/linux-64 5.2MB @ 3.8MB/s 1.4s
pkgs/r/noarch No change
pkgs/main/linux-64 5.5MB @ 3.0MB/s 1.8s
conda-forge/linux-64 30.5MB @ 16.0MB/s 1.9s
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/sgallotti/miniconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 17, in __call__
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/home/sgallotti/miniconda3/lib/python3.11/site-packages/conda_env/cli/main.py", line 56, in do_call
exit_code = getattr(module, func_name)(arguments, parser)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sgallotti/miniconda3/lib/python3.11/site-packages/conda/notices/core.py", line 119, in wrapper
return_value = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/home/sgallotti/miniconda3/lib/python3.11/site-packages/conda_env/cli/main_create.py", line 164, in execute
result[installer_type] = installer.install(
^^^^^^^^^^^^^^^^^^
File "/home/sgallotti/miniconda3/lib/python3.11/site-packages/mamba/mamba_env.py", line 54, in mamba_install
index = load_channels(pool, channel_urls, repos, prepend=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sgallotti/miniconda3/lib/python3.11/site-packages/mamba/utils.py", line 126, in load_channels
index = get_index(
^^^^^^^^^^
File "/home/sgallotti/miniconda3/lib/python3.11/site-packages/mamba/utils.py", line 107, in get_index
is_downloaded = dlist.download(api.MAMBA_DOWNLOAD_FAILFAST)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: Download error (60) SSL peer certificate or SSH remote key was not OK [https://packages.qiime2.org/qiime2/2023.9/amplicon/released/noarch/repodata.json]
SSL certificate problem: unable to get local issuer certificate
$ /home/sgallotti/miniconda3/bin/mamba create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml
environment variables:
CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/sgallotti/miniconda3/bin/conda
CONDA_PREFIX=/home/sgallotti/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/sgallotti/miniconda3/bin/python
CONDA_ROOT=/home/sgallotti/miniconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=
LD_PRELOAD=
PATH=/home/sgallotti/miniconda3/bin:/home/sgallotti/miniconda3/condabin:/us
r/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/
usr/local/games:/usr/lib/wsl/lib:/mnt/c/WINDOWS/system32:/mnt/c/WINDOW
S:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShe
ll/v1.0:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Program Files
(x86)/Pulse Secure/VC142.CRT/X64:/mnt/c/Program Files (x86)/Pulse
Secure/VC142.CRT/X86:/mnt/c/Program Files (x86)/Common Files/Pulse
Secure/VC142.CRT/X64:/mnt/c/Program Files (x86)/Common Files/Pulse
Secure/VC142.CRT/X64:/mnt/c/Program Files (x86)/Common Files/Pulse
Secure/VC142.CRT/X86:/mnt/c/Program Files (x86)/Common Files/Pulse
Secure/TNC Client Plugin:/mnt/c/Program Files
(x86)/REFPROP:/mnt/c/Program Files/dotnet:/mnt/c/Users/sgallotti/AppDa
ta/Local/Microsoft/WindowsApps:/snap/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
active environment : base
active env location : /home/sgallotti/miniconda3
shell level : 1
user config file : /home/sgallotti/.condarc
populated config files : /home/sgallotti/.condarc
conda version : 23.10.0
conda-build version : not installed
python version : 3.11.6.final.0
virtual packages : __archspec=1=skylake
__glibc=2.35=0
__linux=5.10.16.3=0
__unix=0=0
base environment : /home/sgallotti/miniconda3 (writable)
conda av data dir : /home/sgallotti/miniconda3/etc/conda
conda av metadata url : None
channel URLs : conda-forge/linux-64
conda-forge/noarch
main/linux-64
main/noarch
r/linux-64
r/noarch
package cache : /home/sgallotti/miniconda3/pkgs
/home/sgallotti/.conda/pkgs
envs directories : /home/sgallotti/miniconda3/envs
/home/sgallotti/.conda/envs
platform : linux-64
user-agent : conda/23.10.0 requests/2.31.0 CPython/3.11.6 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/22.04.3 glibc/2.35 solver/libmamba conda-libmamba-solver/23.11.0 libmambapy/1.5.3
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If you suspect this error is being caused by a malfunctioning plugin,
consider using the --no-plugins option to turn off plugins.
Example: conda --no-plugins install
Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
the command line to run the command without plugins enabled.
Example: CONDA_NO_PLUGINS=true conda install
Thanks for all your help!
- Matt
