"ValueError: Path: 'None' already exists and is not a cache" when converting file formats

User Support
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1

Here's my command:

qiime tools export --input-path dada2-ccs_table_merged.qza --output-path .

Here's my error:

Traceback (most recent call last):
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/lib/python3.8/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/lib/python3.8/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/lib/python3.8/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 49, in export_data
    result = qiime2.sdk.Result.load(input_path)
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/lib/python3.8/site-packages/qiime2/sdk/result.py", line 67, in load
    archiver = archive.Archiver.load(filepath)
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 342, in load
    path, process_alias, cache = cls._make_temp_path(archive.uuid)
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 274, in _make_temp_path
    cache = get_cache()
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/lib/python3.8/site-packages/qiime2/core/cache.py", line 67, in get_cache
    _CACHE.temp_cache = Cache()
  File "/Users/jespinoz/anaconda3/envs/qiime2_env/lib/python3.8/site-packages/qiime2/core/cache.py", line 176, in __init__
    raise ValueError(f"Path: \'{path}\' already exists and is not a"
ValueError: Path: 'None' already exists and is not a cache

Here's my versions:

System versions
Python version: 3.8.13
QIIME 2 release: 2022.8
QIIME 2 version: 2022.8.1
q2cli version: 2022.8.0

Installed plugins
alignment: 2022.8.0
composition: 2022.8.0
cutadapt: 2022.8.0
dada2: 2022.8.0
deblur: 2022.8.0
demux: 2022.8.0
diversity: 2022.8.0
diversity-lib: 2022.8.0
emperor: 2022.8.0
feature-classifier: 2022.8.0
feature-table: 2022.8.0
fragment-insertion: 2022.8.0
gneiss: 2022.8.0
longitudinal: 2022.8.0
metadata: 2022.8.0
phylogeny: 2022.8.0
quality-control: 2022.8.0
quality-filter: 2022.8.0
sample-classifier: 2022.8.0
taxa: 2022.8.0
types: 2022.8.0
vsearch: 2022.8.0

Application config directory
/Users/jespinoz/anaconda3/envs/qiime2_env/var/q2cli

Getting help
To get help with QIIME 2, visit https://qiime2.org
2

Hello Josh,

Looks like this is the bug mentioned here.

Try updating your version of Qiime2, perhaps to 2022.8.1 or the newest version where the bug should be fixed.

3

I tried running conda clean --all -y and conda update --all -y then created a new environment with the newest build for Mac but now I'm getting this error:

ERROR conda.core.link:_execute(740): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'.
Rolling back transaction: done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0
location of failed script: /Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout:
stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
++ dirname -- /Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/installBiocDataPackage.sh
+ SCRIPT_DIR=/Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages
+ json=/Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.9".fn' /Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
+ FN='"GenomeInfoDbData_1.2.9.tar.gz"'
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".urls[]' /Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".md5' /Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
+ MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
+ STAGING=/Users/jespinoz/anaconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9
+ mkdir -p /Users/jespinoz/anaconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9
+ TARBALL='/Users/jespinoz/anaconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
+ SUCCESS=0
+ for URL in '${URLS[@]}'
++ echo '"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
++ echo '"7cc138cfb74665fdfa8d1c244eac4879"'
++ tr -d '"'
+ MD5=7cc138cfb74665fdfa8d1c244eac4879
+ curl -L https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   416  100   416    0     0    675      0 --:--:-- --:--:-- --:--:--   676
  0     0    0     0    0     0      0      0 --:--:--  0:01:18 --:--:--     0
curl: (7) Failed to connect to mghp.osn.xsede.org port 443 after 77731 ms: Couldn't connect to server

return code: 7

kwargs:
{}

Traceback (most recent call last):
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1132, in __call__
    return func(*args, **kwargs)
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 78, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/notices/core.py", line 121, in wrapper
    return func(*args, **kwargs)
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 152, in execute
    result[installer_type] = installer.install(prefix, pkg_specs, args, env)
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/mamba/mamba_env.py", line 173, in mamba_install
    handle_txn(conda_transaction, prefix, args, True)
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/mamba/linking.py", line 44, in handle_txn
    unlink_link_transaction.execute()
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/core/link.py", line 283, in execute
    self._execute(tuple(chain(*chain(*zip(*self.prefix_action_groups.values())))))
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/core/link.py", line 756, in _execute
    raise CondaMultiError(
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0
location of failed script: /Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout:
stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
++ dirname -- /Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/installBiocDataPackage.sh
+ SCRIPT_DIR=/Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages
+ json=/Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
++ yq '."genomeinfodbdata-1.2.9".fn' /Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
+ FN='"GenomeInfoDbData_1.2.9.tar.gz"'
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".urls[]' /Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
+ URLS+=($value)
+ IFS=
+ read -r value
++ yq '."genomeinfodbdata-1.2.9".md5' /Users/jespinoz/anaconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
+ MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
+ STAGING=/Users/jespinoz/anaconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9
+ mkdir -p /Users/jespinoz/anaconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9
+ TARBALL='/Users/jespinoz/anaconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
+ SUCCESS=0
+ for URL in '${URLS[@]}'
++ echo '"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"'
++ tr -d '"'
+ URL=https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
++ echo '"7cc138cfb74665fdfa8d1c244eac4879"'
++ tr -d '"'
+ MD5=7cc138cfb74665fdfa8d1c244eac4879
+ curl -L https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   416  100   416    0     0    675      0 --:--:-- --:--:-- --:--:--   676
  0     0    0     0    0     0      0      0 --:--:--  0:01:18 --:--:--     0
curl: (7) Failed to connect to mghp.osn.xsede.org port 443 after 77731 ms: Couldn't connect to server

return code: 7

kwargs:
{}

: <exception str() failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/jespinoz/anaconda3/bin/mamba", line 11, in <module>
    sys.exit(main())
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/mamba/mamba.py", line 929, in main
    return mamba_env.main()
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/mamba/mamba_env.py", line 196, in main
    return conda_env_main()
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 89, in main
    return conda_exception_handler(do_call, args, parser)
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1432, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1135, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1164, in handle_exception
    return self.handle_application_exception(exc_val, exc_tb)
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1178, in handle_application_exception
    self._print_conda_exception(exc_val, exc_tb)
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1182, in _print_conda_exception
    print_conda_exception(exc_val, exc_tb)
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1109, in print_conda_exception
    stderrlog.error("\n%r\n", exc_val)
  File "/Users/jespinoz/anaconda3/lib/python3.9/logging/__init__.py", line 1475, in error
    self._log(ERROR, msg, args, **kwargs)
  File "/Users/jespinoz/anaconda3/lib/python3.9/logging/__init__.py", line 1589, in _log
    self.handle(record)
  File "/Users/jespinoz/anaconda3/lib/python3.9/logging/__init__.py", line 1598, in handle
    if (not self.disabled) and self.filter(record):
  File "/Users/jespinoz/anaconda3/lib/python3.9/logging/__init__.py", line 806, in filter
    result = f.filter(record)
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/gateways/logging.py", line 48, in filter
    record.msg = record.msg % new_args
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/__init__.py", line 99, in __repr__
    errs.append(e.__repr__())
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/__init__.py", line 54, in __repr__
    return f"{self.__class__.__name__}: {self}"
  File "/Users/jespinoz/anaconda3/lib/python3.9/site-packages/conda/__init__.py", line 58, in __str__
    return str(self.message % self._kwargs)
ValueError: unsupported format character 'T' (0x54) at index 2114
4

Thanks for trying that!

It looks like the core error is

curl: (7) Failed to connect to mghp.osn.xsede.org port 443 after 77731 ms: Couldn't connect to server

I thought that was fixed based on this thread...

Nevermind, this is a new issue on OSX: QIIME2 native installation error on MacOS

5

Really hoping this gets resolved soon, but I'm glad I'm not the only one encountering this issue

6

So we don't have two threads for one bug, I'll close this one and we can track it in the first thread.

(As always, you can both open new threads about new issues :person_raising_hand:)

Thanks for sharing what you found about that bug and helping us Keep it Tidy :broom: