QIIME2 installation problem

[adriansh]

Hello everyone!
I use ubuntu 23.10 and I tried to install QIIME2 Amplicon Distribution using Conda.
I followed the installation guide and after 'conda env create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-linux-conda.yml' I got an error:

Collecting package metadata (repodata.json): done
Solving environment: failed
Channels:
 - https://packages.qiime2.org/qiime2/2024.2/amplicon/released
 - bioconda
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package bleach-6.1.0-pyhd8ed1ab_0 is excluded by strict repo priority
  - package c-ares-1.27.0-hd590300_0 is excluded by strict repo priority
  - package glpk-5.0-h445213a_0 is excluded by strict repo priority
  - package jq-1.7.1-hd590300_0 is excluded by strict repo priority
  - package tqdm-4.66.2-pyhd8ed1ab_0 is excluded by strict repo priority
  - package argh-0.31.2-pyhd8ed1ab_0 is excluded by strict repo priority
  - package bioconductor-delayedmatrixstats-1.20.0-r42hdfd78af_0 requires r-matrixstats >=0.60.0, but none of the providers can be installed
  - package bioconductor-phyloseq-1.42.0-r42hdfd78af_0 requires r-ade4 >=1.7-4, but none of the providers can be installed
  - package deblur-1.1.1-pyhdfd78af_0 requires scikit-bio >=0.5.0, but none of the providers can be installed
  - package ncbi-datasets-pylib-16.6.0-pyhdfd78af_0 requires urllib3 1.26.*, but none of the providers can be installed
  - package paramiko-3.4.0-pyhd8ed1ab_0 requires pynacl >=1.5, but none of the providers can be installed
  - package q2-composition-2024.2.0-py38h898cb5b_0 requires biom-format 2.1.14.*, but none of the providers can be installed
  - package q2-dada2-2024.2.0-py38h45c52d9_0 requires r-optparse >=1.7.1, but none of the providers can be installed
  - package q2-emperor-2024.2.0-py38h2998407_0 requires emperor 1.0.4, but none of the providers can be installed
  - package yq-3.2.3-pyhd8ed1ab_0 requires xmltodict >=0.11.0, but none of the providers can be installed
  - package biopython-1.83-py39hf860d4a_0 is excluded by strict repo priority
  - package libdb-6.2.32-hf484d3e_0 is excluded by strict repo priority
  - package libdeflate-1.17-h5eee18b_1 is excluded by strict repo priority
  - package munkres-1.1.4-py_0 is excluded by strict repo priority
  - package r-bh-1.84.0_0-r43hc72bb7e_0 is excluded by strict repo priority
  - package r-bit-4.0.5-r43h76d94ec_0 is excluded by strict repo priority
  - package r-bit64-4.0.5-r43h76d94ec_0 is excluded by strict repo priority
  - package r-checkmate-2.3.0-r43h76d94ec_0 is excluded by strict repo priority
  - package r-data.table-1.15.2-r43h029312a_0 is excluded by strict repo priority
  - package r-deldir-2.0_4-r43h61816a4_0 is excluded by strict repo priority
  - package r-digest-0.6.34-r43ha503ecb_0 is excluded by strict repo priority
  - package r-dorng-1.8.6-r43h142f84f_0 is excluded by strict repo priority
  - package r-dplyr-1.1.4-r43ha503ecb_0 is excluded by strict repo priority
  - package r-e1071-1.7_14-r43ha503ecb_0 is excluded by strict repo priority
  - package r-fnn-1.1.4-r43ha503ecb_0 is excluded by strict repo priority
  - package r-futile.logger-1.4.3-r43h6115d3f_0 is excluded by strict repo priority
  - package r-futile.options-1.0.1-r43h142f84f_0 is excluded by strict repo priority
  - package r-ggplot2-3.5.0-r43hc72bb7e_0 is excluded by strict repo priority
  - package r-ggrepel-0.9.5-r43ha503ecb_0 is excluded by strict repo priority
  - package r-htmltools-0.5.7-r43ha503ecb_0 is excluded by strict repo priority
  - package r-htmlwidgets-1.6.4-r43hc72bb7e_1 is excluded by strict repo priority
  - package r-hwriter-1.3.2.1-r43h142f84f_0 is excluded by strict repo priority
  - package r-jpeg-0.1_10-r43h76d94ec_1 is excluded by strict repo priority
  - package r-jsonlite-1.8.8-r43h57805ef_0 is excluded by strict repo priority
  - package r-knitr-1.45-r43hc72bb7e_1 is excluded by strict repo priority
  - package r-lambda.r-1.2.4-r43h142f84f_0 is excluded by strict repo priority
  - package r-magrittr-2.0.3-r43h76d94ec_0 is excluded by strict repo priority
  - package r-permute-0.9_7-r43h142f84f_0 is excluded by strict repo priority
  - package r-pheatmap-1.0.12-r43h142f84f_0 is excluded by strict repo priority
  - package r-png-0.1_8-r43h76d94ec_0 is excluded by strict repo priority
  - package r-prettyunits-1.2.0-r43h142f84f_0 is excluded by strict repo priority
  - package r-progress-1.2.3-r43hc72bb7e_0 is excluded by strict repo priority
  - package r-proxy-0.4_27-r43h76d94ec_0 is excluded by strict repo priority
  - package r-rappdirs-0.3.3-r43h76d94ec_0 is excluded by strict repo priority
  - package r-rcppparallel-5.1.6-r43ha503ecb_1 is excluded by strict repo priority
  - package r-readr-2.1.5-r43ha503ecb_0 is excluded by strict repo priority
  - package r-rematch2-2.1.2-r43h142f84f_0 is excluded by strict repo priority
  - package r-rmarkdown-2.25-r43h6115d3f_0 is excluded by strict repo priority
  - package r-rtsne-0.17-r43h7ce84a7_0 is excluded by strict repo priority
  - package r-scales-1.3.0-r43hc72bb7e_0 is excluded by strict repo priority
  - package r-snow-0.4_4-r43h142f84f_0 is excluded by strict repo priority
  - package r-statmod-1.5.0-r43h640688f_0 is excluded by strict repo priority
  - package r-stringr-1.5.1-r43h785f33e_0 is excluded by strict repo priority
  - package r-tibble-3.2.1-r43h76d94ec_0 is excluded by strict repo priority
  - package r-vegan-2.6_4-r43h640688f_0 is excluded by strict repo priority
  - package r-viridis-0.6.5-r43hc72bb7e_0 is excluded by strict repo priority
  - package r-yaml-2.3.8-r43h57805ef_0 is excluded by strict repo priority
  - package simplejson-3.19.2-py39hf860d4a_0 is excluded by strict repo priority
  - package xopen-1.9.0-py39hf3d152e_0 is excluded by strict repo priority
  - package libnghttp2-1.52.0-h61bc06f_0 requires openssl >=3.0.8,<4.0a0, but none of the providers can be installed
  - package htslib-1.17-h6bc39ce_0 requires openssl >=1.1.1t,<1.1.2a, but none of the providers can be installed

Is this Conda or QIIME2 problem?

[jphagen (Johannah Hagen)]

Hi @adriansh,

Welcome to the forum!

This looks like a conda problem...
I was able to find this post on stack overflow regarding this strict repo priority erorr which suggests that your conda configurations are causing the problem.

Can you run conda config --show and post the full output here.

--Hannah

[adriansh]

Thank you for your help.
This is my output:

add_anaconda_token: True
add_pip_as_python_dependency: True
aggressive_update_packages:
  - ca-certificates
  - certifi
  - openssl
allow_conda_downgrades: True
allow_cycles: True
allow_non_channel_urls: False
allow_softlinks: False
allowlist_channels: []
always_copy: False
always_softlink: False
always_yes: None
anaconda_upload: None
auto_activate_base: True
auto_stack: 0
auto_update_conda: True
bld_path: 
changeps1: True
channel_alias: https://conda.anaconda.org
channel_priority: strict
channel_settings: []
channels:
  - conda-forge
  - bioconda
  - defaults
client_ssl_cert: None
client_ssl_cert_key: None
clobber: False
conda_build: {}
create_default_packages: []
croot: /home/ewewe/miniconda3/conda-bld
custom_channels:
  pkgs/main: https://repo.anaconda.com
  pkgs/r: https://repo.anaconda.com
  pkgs/pro: https://repo.anaconda.com
custom_multichannels:
  defaults: 
    - https://repo.anaconda.com/pkgs/main
    - https://repo.anaconda.com/pkgs/r
  local: 
debug: False
default_channels:
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
default_python: 3.12
default_threads: None
deps_modifier: not_set
dev: False
disallowed_packages: []
download_only: False
dry_run: False
enable_private_envs: False
env_prompt: ({default_env}) 
envs_dirs:
  - /home/ewewe/miniconda3/envs
  - /home/ewewe/.conda/envs
error_upload_url: https://conda.io/conda-post/unexpected-error
execute_threads: 1
experimental: []
extra_safety_checks: False
fetch_threads: 5
force: False
force_32bit: False
force_reinstall: False
force_remove: False
ignore_pinned: False
json: False
local_repodata_ttl: 1
migrated_channel_aliases: []
migrated_custom_channels: {}
no_lock: False
no_plugins: False
non_admin_enabled: True
notify_outdated_conda: True
number_channel_notices: 5
offline: False
override_channels_enabled: True
path_conflict: clobber
pinned_packages: []
pip_interop_enabled: False
pkgs_dirs:
  - /home/ewewe/miniconda3/pkgs
  - /home/ewewe/.conda/pkgs
proxy_servers: {}
quiet: False
register_envs: True
remote_backoff_factor: 1
remote_connect_timeout_secs: 9.15
remote_max_retries: 3
remote_read_timeout_secs: 60.0
repodata_fns:
  - current_repodata.json
  - repodata.json
repodata_threads: None
repodata_use_zst: True
report_errors: None
restore_free_channel: False
rollback_enabled: True
root_prefix: /home/ewewe/miniconda3
safety_checks: warn
sat_solver: pycosat
separate_format_cache: False
shortcuts: True
shortcuts_only: []
show_channel_urls: True
signing_metadata_url_base: None
solver: libmamba
solver_ignore_timestamps: False
ssl_verify: True
subdir: linux-64
subdirs:
  - linux-64
  - noarch
target_prefix_override: 
trace: False
track_features: []
unsatisfiable_hints: True
unsatisfiable_hints_check_depth: 2
update_modifier: update_specs
use_index_cache: False
use_local: False
use_only_tar_bz2: False
verbosity: 0
verify_threads: 1

[jphagen (Johannah Hagen)]

Okay great!

Please run conda config --set channel_priority flexible then re run your environment command and it should work this time. If not I will be here to help

--Hannah

[adriansh]

@jphagen

conda config --set channel_priority flexible

Thank you so much!
It works now <3