Hi! I am trying to install qiime2 natively in conda environment on my macbook air. When I get to this step in installation:
conda env create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-osx-conda.yml
I get many dependency errors.
conda config --show
add_anaconda_token: True
add_pip_as_python_dependency: True
aggressive_update_packages:
ca-certificates
certifi
openssl
allow_conda_downgrades: False
allow_cycles: True
allow_non_channel_urls: False
allow_softlinks: False
allowlist_channels:
always_copy: False
always_softlink: False
always_yes: None
anaconda_anon_usage: True
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: flexible
channel_settings:
channels:
qiime2
bioconda
conda-forge
defaults
client_ssl_cert: None
client_ssl_cert_key: None
clobber: False
conda_build: {}
create_default_packages:
croot: /opt/anaconda3/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:
local:
debug: False
default_channels:
default_python: 3.11
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:
/opt/anaconda3/envs
/Users/madelaineleitman/.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:
/opt/anaconda3/pkgs
/Users/madelaineleitman/.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: /opt/anaconda3
safety_checks: warn
sat_solver: pycosat
separate_format_cache: False
shortcuts: True
shortcuts_only:
show_channel_urls: None
signing_metadata_url_base: None
solver: libmamba
solver_ignore_timestamps: False
ssl_verify: True
subdir: osx-arm64
subdirs:
osx-arm64
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
Hello @MADELAINE_LEITMAN,
Since you're using an M2 Mac you need to run CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-osx-conda.yml as the docs specify here.
@colinvwood , got it, thank you!
Now after this command:
CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-osx-conda.yml
I get this error:
return code: 18
kwargs:
{}
: <exception str() failed>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/anaconda3/bin/conda", line 13, in
sys.exit(main())
^^^^^^
File "/opt/anaconda3/lib/python3.11/site-packages/conda/cli/main.py", line 127, in main
return conda_exception_handler(main, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 387, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 20, in call
return self.handle_exception(exc_val, exc_tb)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 61, in handle_exception
return self.handle_application_exception(exc_val, exc_tb)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 77, in handle_application_exception
self._print_conda_exception(exc_val, exc_tb)
File "/opt/anaconda3/lib/python3.11/site-packages/conda/exception_handler.py", line 83, in _print_conda_exception
print_conda_exception(exc_val, exc_tb)
File "/opt/anaconda3/lib/python3.11/site-packages/conda/exceptions.py", line 1261, in print_conda_exception
stderrlog.error("\n%r\n", exc_val)
File "/opt/anaconda3/lib/python3.11/logging/init.py", line 1518, in error
self._log(ERROR, msg, args, **kwargs)
File "/opt/anaconda3/lib/python3.11/logging/init.py", line 1634, in _log
self.handle(record)
File "/opt/anaconda3/lib/python3.11/logging/init.py", line 1643, in handle
if (not self.disabled) and self.filter(record):
^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/lib/python3.11/logging/init.py", line 830, in filter
result = f.filter(record)
^^^^^^^^^^^^^^^^
File "/opt/anaconda3/lib/python3.11/site-packages/conda/gateways/logging.py", line 66, in filter
record.msg = record.msg % new_args
~~~^
File "/opt/anaconda3/lib/python3.11/site-packages/conda/init.py", line 104, in repr
errs.append(e.repr())
^^^^^^^^^^^^
File "/opt/anaconda3/lib/python3.11/site-packages/conda/init.py", line 58, in repr
return f"{self.class.name}: {self}"
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/lib/python3.11/site-packages/conda/init.py", line 62, in str
return str(self.message % self._kwargs)
~^
ValueError: unsupported format character 'T' (0x54) at index 2094
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