Error using qiime2 environment since trying to install q2_fondue

[Cecile]

Hello,

I am currently running QIIME 2 (2022.8) on mac os terminal (apple M1 chip). I have install and create the environment last years using conda (with the CONDA_SUBDIR=osx-64 command line) and everything worked fine.

Recently, I have tried to install q2-fondue by following the tutoriel (q2-fondue/README.md at main · bokulich-lab/q2-fondue · GitHub) directely from my qiime environment but it doesn't worked so I tried directly to run the install-sra-tools.sh file (q2-fondue/install-sra-tools.sh at main · bokulich-lab/q2-fondue · GitHub).
I have download the zip file from the github, then I run

bash install-sra-tools.sh
python setup.py install
When I do this it worked and print
(qiime2-2022.8) bash-3.2$ bash install-sra-tools.sh

Fetching SRA Tools from http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.0/sratoolkit.3.0.0-mac64.tar.gz...

% Total % Received % Xferd Average Speed Time Time Time Current

Dload Upload Total Spent Left Speed

100 286 100 286 0 0 582 0 --:--:-- --:--:-- --:--:-- 582

100 77.9M 100 77.9M 0 0 8197k 0 0:00:09 0:00:09 --:--:-- 11.3M

Extracting...

Setting PREFIX=/opt/miniconda3/envs/qiime2-2022.8

Installing SRA Tools in /opt/miniconda3/envs/qiime2-2022.8...

Testing installation...

Success!

Configuring SRA Toolkit:

Creating prefetch cache directory under /Users/cecileblanchon/.prefetch_cache...

mkdir: /Users/cecileblanchon/.prefetch_cache: File exists

Running vdb-config...

Prefetch will download to User Repository when Public User Repository is set

Configuration completed.

(qiime2-2022.8) bash-3.2$ python setup.py install

running install

/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.

warnings.warn(

/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.

warnings.warn(

running bdist_egg

running egg_info

creating q2_fondue.egg-info

writing q2_fondue.egg-info/PKG-INFO

writing dependency_links to q2_fondue.egg-info/dependency_links.txt

writing entry points to q2_fondue.egg-info/entry_points.txt

writing top-level names to q2_fondue.egg-info/top_level.txt

writing manifest file 'q2_fondue.egg-info/SOURCES.txt'

reading manifest file 'q2_fondue.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

adding license file 'LICENSE'

writing manifest file 'q2_fondue.egg-info/SOURCES.txt'

installing library code to build/bdist.macosx-10.9-x86_64/egg

running install_lib

running build_py

creating build

creating build/lib

creating build/lib/q2_fondue

copying q2_fondue/sequences.py -> build/lib/q2_fondue

copying q2_fondue/scraper.py -> build/lib/q2_fondue

copying q2_fondue/get_all.py -> build/lib/q2_fondue

copying q2_fondue/metadata.py -> build/lib/q2_fondue

copying q2_fondue/query.py -> build/lib/q2_fondue

copying q2_fondue/_version.py -> build/lib/q2_fondue

copying q2_fondue/plugin_setup.py -> build/lib/q2_fondue

copying q2_fondue/init.py -> build/lib/q2_fondue

copying q2_fondue/utils.py -> build/lib/q2_fondue

creating build/lib/q2_fondue/types

copying q2_fondue/types/init.py -> build/lib/q2_fondue/types

copying q2_fondue/types/_format.py -> build/lib/q2_fondue/types

copying q2_fondue/types/_type.py -> build/lib/q2_fondue/types

copying q2_fondue/types/_transformer.py -> build/lib/q2_fondue/types

creating build/lib/q2_fondue/entrezpy_clients

copying q2_fondue/entrezpy_clients/init.py -> build/lib/q2_fondue/entrezpy_clients

copying q2_fondue/entrezpy_clients/_sra_meta.py -> build/lib/q2_fondue/entrezpy_clients

copying q2_fondue/entrezpy_clients/_pipelines.py -> build/lib/q2_fondue/entrezpy_clients

copying q2_fondue/entrezpy_clients/_efetch.py -> build/lib/q2_fondue/entrezpy_clients

copying q2_fondue/entrezpy_clients/_esearch.py -> build/lib/q2_fondue/entrezpy_clients

copying q2_fondue/entrezpy_clients/_utils.py -> build/lib/q2_fondue/entrezpy_clients

creating build/lib/q2_fondue/tests

copying q2_fondue/tests/test_get_all.py -> build/lib/q2_fondue/tests

copying q2_fondue/tests/test_utils.py -> build/lib/q2_fondue/tests

copying q2_fondue/tests/test_scraper.py -> build/lib/q2_fondue/tests

copying q2_fondue/tests/test_metadata.py -> build/lib/q2_fondue/tests

copying q2_fondue/tests/init.py -> build/lib/q2_fondue/tests

copying q2_fondue/tests/test_efetch.py -> build/lib/q2_fondue/tests

copying q2_fondue/tests/test_sequences.py -> build/lib/q2_fondue/tests

copying q2_fondue/tests/test_query.py -> build/lib/q2_fondue/tests

copying q2_fondue/tests/test_esearch.py -> build/lib/q2_fondue/tests

copying q2_fondue/tests/test_sra_meta.py -> build/lib/q2_fondue/tests

copying q2_fondue/tests/_utils.py -> build/lib/q2_fondue/tests

creating build/lib/q2_fondue/types/tests

copying q2_fondue/types/tests/init.py -> build/lib/q2_fondue/types/tests

copying q2_fondue/types/tests/test_types_formats_transformers.py -> build/lib/q2_fondue/types/tests

copying q2_fondue/citations.bib -> build/lib/q2_fondue

creating build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testaccA_01_L001_R1_001.fastq -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-exp-5.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-4.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/scraper_items_no_attach.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/elink_response_single.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testaccHYB_1.fastq -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-5.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-exp-4.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/esearch_response_multi_mixed.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/efetch_b1_response_runs.xml -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/esearch_response_multi_invalid.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/SRX123456_md.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/metadata_response_multi.xml -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-7.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-mock.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/metadata_response_small.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/fasterq-dump-response.txt -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-6.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/run_ids_w_doi.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testaccA.fastq -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-exp-3.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/metadata_processed_multi.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-2.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testacc_00_L001_R1_001.fastq -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-3.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/run_ids.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-exp-2.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-1.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/SRR1234567_md.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-exp-1.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/esearch_response_single_ambiguous.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-failed-ids.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/SRR123456.fastq -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testaccA.sra -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/scraper_items_journalarticle.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testaccHYB_2.fastq -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sample_ids_w_doi.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/bioproject_ids.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/scraper_items_no_doi.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/SRS123456_md.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/bioproject_ids_w_doi.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testaccC_md.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/efetch_b2_response_runs.xml -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/metadata_from_xml.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/efetch_response_runs.xml -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/SRR123456_md.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sample_ids.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/SRP123456_md.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/metadata_response_single_complex.xml -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/study_ids_w_doi.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/SRR123457_1.fastq -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/study_ids.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testacc_1.fastq -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testaccHYB.fastq -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/metadata_response_error.xml -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/experiment_ids_w_doi.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/experiment_ids.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/SRR123457_2.fastq -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/failed_ids_no_doi.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/metadata_response_single_multisample.xml -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/esearch_response_multi_correct.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/efetch_response_runs_single_item.xml -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/scraper_items_mix.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/metadata_response_single.xml -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testacc_00_L001_R2_001.fastq -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/SRR123457_md.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/scraper_item_multiple_dois.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/run_ids_w_doi_2.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/SRR123457.sra -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/esearch_response_single_correct.json -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testaccBC_md.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/sra-metadata-8.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testacc_2.fastq -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/SRR123456.sra -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/testaccB_md.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/PRJNA734376_md.tsv -> build/lib/q2_fondue/tests/data

copying q2_fondue/tests/data/scraper_collections.json -> build/lib/q2_fondue/tests/data

creating build/lib/q2_fondue/tests/data/paired2

copying q2_fondue/tests/data/paired2/SEQID3_00_L001_R2_001.fastq.gz -> build/lib/q2_fondue/tests/data/paired2

copying q2_fondue/tests/data/paired2/SEQID4_00_L001_R2_001.fastq.gz -> build/lib/q2_fondue/tests/data/paired2

copying q2_fondue/tests/data/paired2/SEQID4_00_L001_R1_001.fastq.gz -> build/lib/q2_fondue/tests/data/paired2

copying q2_fondue/tests/data/paired2/SEQID3_00_L001_R1_001.fastq.gz -> build/lib/q2_fondue/tests/data/paired2

creating build/lib/q2_fondue/tests/data/empty

copying q2_fondue/tests/data/empty/xxx_00_L001_R1_001.fastq.gz -> build/lib/q2_fondue/tests/data/empty

copying q2_fondue/tests/data/empty/xxx_00_L001_R2_001.fastq.gz -> build/lib/q2_fondue/tests/data/empty

creating build/lib/q2_fondue/tests/data/single1

copying q2_fondue/tests/data/single1/SEQID1_00_L001_R1_001.fastq.gz -> build/lib/q2_fondue/tests/data/single1

copying q2_fondue/tests/data/single1/SEQID2_00_L001_R1_001.fastq.gz -> build/lib/q2_fondue/tests/data/single1

creating build/lib/q2_fondue/tests/data/paired1

copying q2_fondue/tests/data/paired1/SEQID1_00_L001_R1_001.fastq.gz -> build/lib/q2_fondue/tests/data/paired1

copying q2_fondue/tests/data/paired1/SEQID2_00_L001_R1_001.fastq.gz -> build/lib/q2_fondue/tests/data/paired1

copying q2_fondue/tests/data/paired1/SEQID2_00_L001_R2_001.fastq.gz -> build/lib/q2_fondue/tests/data/paired1

copying q2_fondue/tests/data/paired1/SEQID1_00_L001_R2_001.fastq.gz -> build/lib/q2_fondue/tests/data/paired1

creating build/lib/q2_fondue/tests/data/single2

copying q2_fondue/tests/data/single2/SEQID4_00_L001_R1_001.fastq.gz -> build/lib/q2_fondue/tests/data/single2

copying q2_fondue/tests/data/single2/SEQID3_00_L001_R1_001.fastq.gz -> build/lib/q2_fondue/tests/data/single2

creating build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/ncbi-ids-runs-doi.tsv -> build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/ncbi-ids-runs.tsv -> build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/ncbi-ids-wrong.tsv -> build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/sra-metadata.tsv -> build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/ncbi-ids-runs-wrong-id-header.tsv -> build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/sra-metadata-missing-ids.tsv -> build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/sra-failed-ids-empty.tsv -> build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/sra-failed-ids.tsv -> build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/sra-metadata-missing-columns.tsv -> build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/ncbi-ids-studies.tsv -> build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/ncbi-ids-other.tsv -> build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/ncbi-ids-bioprojects.tsv -> build/lib/q2_fondue/types/tests/data

copying q2_fondue/types/tests/data/ncbi-ids-runs-no-doi.tsv -> build/lib/q2_fondue/types/tests/data

UPDATING build/lib/q2_fondue/_version.py

set build/lib/q2_fondue/_version.py to '0+unknown'

creating build/bdist.macosx-10.9-x86_64

creating build/bdist.macosx-10.9-x86_64/egg

creating build/bdist.macosx-10.9-x86_64/egg/q2_fondue

copying build/lib/q2_fondue/sequences.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue

copying build/lib/q2_fondue/scraper.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue

creating build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types

creating build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests

copying build/lib/q2_fondue/types/tests/init.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests

copying build/lib/q2_fondue/types/tests/test_types_formats_transformers.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests

creating build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/ncbi-ids-runs-doi.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/ncbi-ids-runs.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/ncbi-ids-wrong.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/sra-metadata.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/ncbi-ids-runs-wrong-id-header.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/sra-metadata-missing-ids.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/sra-failed-ids-empty.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/sra-failed-ids.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/sra-metadata-missing-columns.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/ncbi-ids-studies.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/ncbi-ids-other.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/ncbi-ids-bioprojects.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/tests/data/ncbi-ids-runs-no-doi.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/data

copying build/lib/q2_fondue/types/init.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types

copying build/lib/q2_fondue/types/_format.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types

copying build/lib/q2_fondue/types/_type.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types

copying build/lib/q2_fondue/types/_transformer.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types

copying build/lib/q2_fondue/get_all.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue

copying build/lib/q2_fondue/metadata.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue

copying build/lib/q2_fondue/query.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue

copying build/lib/q2_fondue/_version.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue

creating build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients

copying build/lib/q2_fondue/entrezpy_clients/init.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients

copying build/lib/q2_fondue/entrezpy_clients/_sra_meta.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients

copying build/lib/q2_fondue/entrezpy_clients/_pipelines.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients

copying build/lib/q2_fondue/entrezpy_clients/_efetch.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients

copying build/lib/q2_fondue/entrezpy_clients/_esearch.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients

copying build/lib/q2_fondue/entrezpy_clients/_utils.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients

creating build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests

copying build/lib/q2_fondue/tests/test_get_all.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests

copying build/lib/q2_fondue/tests/test_utils.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests

copying build/lib/q2_fondue/tests/test_scraper.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests

copying build/lib/q2_fondue/tests/test_metadata.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests

copying build/lib/q2_fondue/tests/init.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests

copying build/lib/q2_fondue/tests/test_efetch.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests

copying build/lib/q2_fondue/tests/test_sequences.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests

copying build/lib/q2_fondue/tests/test_query.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests

copying build/lib/q2_fondue/tests/test_esearch.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests

creating build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testaccA_01_L001_R1_001.fastq -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-exp-5.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-4.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/scraper_items_no_attach.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/elink_response_single.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testaccHYB_1.fastq -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-5.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-exp-4.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/esearch_response_multi_mixed.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/efetch_b1_response_runs.xml -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/esearch_response_multi_invalid.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/SRX123456_md.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/metadata_response_multi.xml -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-7.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-mock.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/metadata_response_small.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/fasterq-dump-response.txt -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-6.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

creating build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/paired2

copying build/lib/q2_fondue/tests/data/paired2/SEQID3_00_L001_R2_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/paired2

copying build/lib/q2_fondue/tests/data/paired2/SEQID4_00_L001_R2_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/paired2

copying build/lib/q2_fondue/tests/data/paired2/SEQID4_00_L001_R1_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/paired2

copying build/lib/q2_fondue/tests/data/paired2/SEQID3_00_L001_R1_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/paired2

copying build/lib/q2_fondue/tests/data/run_ids_w_doi.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testaccA.fastq -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-exp-3.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/metadata_processed_multi.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-2.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testacc_00_L001_R1_001.fastq -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-3.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/run_ids.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-exp-2.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

creating build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/empty

copying build/lib/q2_fondue/tests/data/empty/xxx_00_L001_R1_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/empty

copying build/lib/q2_fondue/tests/data/empty/xxx_00_L001_R2_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/empty

copying build/lib/q2_fondue/tests/data/sra-metadata-1.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/SRR1234567_md.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-exp-1.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/esearch_response_single_ambiguous.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-failed-ids.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/SRR123456.fastq -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testaccA.sra -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/scraper_items_journalarticle.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testaccHYB_2.fastq -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sample_ids_w_doi.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/bioproject_ids.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/scraper_items_no_doi.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/SRS123456_md.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/bioproject_ids_w_doi.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testaccC_md.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/efetch_b2_response_runs.xml -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/metadata_from_xml.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/efetch_response_runs.xml -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/SRR123456_md.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

creating build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/single1

copying build/lib/q2_fondue/tests/data/single1/SEQID1_00_L001_R1_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/single1

copying build/lib/q2_fondue/tests/data/single1/SEQID2_00_L001_R1_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/single1

copying build/lib/q2_fondue/tests/data/sample_ids.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/SRP123456_md.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

creating build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/paired1

copying build/lib/q2_fondue/tests/data/paired1/SEQID1_00_L001_R1_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/paired1

copying build/lib/q2_fondue/tests/data/paired1/SEQID2_00_L001_R1_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/paired1

copying build/lib/q2_fondue/tests/data/paired1/SEQID2_00_L001_R2_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/paired1

copying build/lib/q2_fondue/tests/data/paired1/SEQID1_00_L001_R2_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/paired1

copying build/lib/q2_fondue/tests/data/metadata_response_single_complex.xml -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/study_ids_w_doi.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/SRR123457_1.fastq -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/study_ids.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testacc_1.fastq -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testaccHYB.fastq -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/metadata_response_error.xml -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/experiment_ids_w_doi.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/experiment_ids.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/SRR123457_2.fastq -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/failed_ids_no_doi.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/metadata_response_single_multisample.xml -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/esearch_response_multi_correct.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/efetch_response_runs_single_item.xml -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/scraper_items_mix.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/metadata_response_single.xml -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testacc_00_L001_R2_001.fastq -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/SRR123457_md.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/scraper_item_multiple_dois.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/run_ids_w_doi_2.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/SRR123457.sra -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

creating build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/single2

copying build/lib/q2_fondue/tests/data/single2/SEQID4_00_L001_R1_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/single2

copying build/lib/q2_fondue/tests/data/single2/SEQID3_00_L001_R1_001.fastq.gz -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data/single2

copying build/lib/q2_fondue/tests/data/esearch_response_single_correct.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testaccBC_md.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/sra-metadata-8.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testacc_2.fastq -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/SRR123456.sra -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/testaccB_md.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/PRJNA734376_md.tsv -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/data/scraper_collections.json -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/data

copying build/lib/q2_fondue/tests/test_sra_meta.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests

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copying build/lib/q2_fondue/init.py -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue

copying build/lib/q2_fondue/citations.bib -> build/bdist.macosx-10.9-x86_64/egg/q2_fondue

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byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/sequences.py to sequences.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/scraper.py to scraper.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/init.py to init.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/tests/test_types_formats_transformers.py to test_types_formats_transformers.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/init.py to init.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/types/_format.py to _format.cpython-38.pyc

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byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/get_all.py to get_all.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/metadata.py to metadata.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/query.py to query.cpython-38.pyc

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byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients/init.py to init.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients/_sra_meta.py to _sra_meta.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients/_pipelines.py to _pipelines.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients/_efetch.py to _efetch.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients/_esearch.py to _esearch.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/entrezpy_clients/_utils.py to _utils.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/test_get_all.py to test_get_all.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/test_utils.py to test_utils.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/test_scraper.py to test_scraper.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/test_metadata.py to test_metadata.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/init.py to init.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/test_efetch.py to test_efetch.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/test_sequences.py to test_sequences.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/test_query.py to test_query.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/test_esearch.py to test_esearch.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/test_sra_meta.py to test_sra_meta.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/tests/_utils.py to _utils.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/plugin_setup.py to plugin_setup.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/init.py to init.cpython-38.pyc

byte-compiling build/bdist.macosx-10.9-x86_64/egg/q2_fondue/utils.py to utils.cpython-38.pyc

creating build/bdist.macosx-10.9-x86_64/egg/EGG-INFO

copying q2_fondue.egg-info/PKG-INFO -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO

copying q2_fondue.egg-info/SOURCES.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO

copying q2_fondue.egg-info/dependency_links.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO

copying q2_fondue.egg-info/entry_points.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO

copying q2_fondue.egg-info/not-zip-safe -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO

copying q2_fondue.egg-info/top_level.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO

creating dist

creating 'dist/q2_fondue-0+unknown-py3.8.egg' and adding 'build/bdist.macosx-10.9-x86_64/egg' to it

removing 'build/bdist.macosx-10.9-x86_64/egg' (and everything under it)

Processing q2_fondue-0+unknown-py3.8.egg

removing '/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_fondue-0+unknown-py3.8.egg' (and everything under it)

creating /opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_fondue-0+unknown-py3.8.egg

Extracting q2_fondue-0+unknown-py3.8.egg to /opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages

q2-fondue 0+unknown is already the active version in easy-install.pth

Installed /opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_fondue-0+unknown-py3.8.egg

Processing dependencies for q2-fondue==0+unknown

Finished processing dependencies for q2-fondue==0+unknown

When I tried to verified package information using conda list, I see that the q2-fondue package was not install correctly (version 0+unknown, build pypi_0 and channel pypi) Since, whatever the qiime commande that I tried to achive, it doesn't work...
(qiime2-2022.8) bash-3.2$ qiime info
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/util.py", line 224, in get_plugin_manager
return qiime2.sdk.PluginManager.reuse_existing()
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 58, in reuse_existing
raise UninitializedPluginManagerError
qiime2.sdk.plugin_manager.UninitializedPluginManagerError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/miniconda3/envs/qiime2-2022.8/bin/qiime", line 11, in
sys.exit(qiime())
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/builtin/info.py", line 44, in info
import q2cli.core.cache
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/core/cache.py", line 285, in
CACHE = DeploymentCache()
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/core/cache.py", line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/core/cache.py", line 205, in _cache_current_state
state = self._get_current_state()
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/core/cache.py", line 253, in _get_current_state
plugin_manager = q2cli.util.get_plugin_manager()
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/util.py", line 236, in get_plugin_manager
return qiime2.sdk.PluginManager()
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 67, in new
self._init(add_plugins=add_plugins)
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init
plugin = entry_point.load()
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/pkg_resources/init.py", line 2471, in load
return self.resolve()
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/pkg_resources/init.py", line 2477, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_fondue-0+unknown-py3.8.egg/q2_fondue/plugin_setup.py", line 20, in
from q2_fondue.get_all import get_all
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_fondue-0+unknown-py3.8.egg/q2_fondue/get_all.py", line 14, in
from q2_fondue.utils import handle_threaded_exception
File "/opt/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2_fondue-0+unknown-py3.8.egg/q2_fondue/utils.py", line 15, in
from entrezpy.esearch import esearcher as es
ModuleNotFoundError: No module named 'entrezpy'

Could you help me pleased, I am new on conda and qiime...

Cecile

[Nicholas_Bokulich]

Hi @Cecile ,

Welcome to the QIIME 2 forum, and thanks for using q2-fondue!

As you can see, attempting a "manual installation" of the various dependencies can get very messy and so is not recommended (basically you will go down a rabbit hole of one dependency to another ).

So I strongly recommend getting one of the standard installation instructions to work instead.

But I have good news: not yet added to the q2-fondue installation instructions is the fact that q2-fondue is already part of one of the standard QIIME 2 distributions (the shotgun distribution) since 2024.2... so a very easy way to install now would be to simply install the QIIME 2 shotgun distribution following the instructions on the QIIME 2 documents.

I hope that helps!

[Cecile]

Hi @Nicholas_Bokulich ,

I have already try to install the new QIIME 2 distribution but since I have try to install q2-fondue I can't create a new environment with conda.

bash-3.2$ curl -sL "https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.2-py38-osx-conda.yml" > "qiime2-shotgun-2024.2-py38-osx-conda.ylm"
bash-3.2$ CONDA_SUBDIR=osx-64 conda env create -n qiime2-shotgun-2024.2 --file qiime2-shotgun-2024.2-py38-osx-conda.yml

I always get this error

failed
CondaSSLError: OpenSSL appears to be unavailable on this machine. OpenSSL is required to download and install packages.
Exception: HTTPSConnectionPool(host='packages.qiime2.org', port=443): Max retries exceeded with url: /qiime2/2024.2/shotgun/released/osx-64/repodata.json (Caused by SSLError("Can't connect to HTTPS URL because the SSL module is not available."))

[Nicholas_Bokulich]

Hi @Cecile ,

It looks like your conda installation might have been messed up if it is not allowing you to create new environments; see the responses on this topic to troubleshoot:

Error Installing QIIME2!

Hi! I have a Mac with an M2 chip and I'm currently trying to install the latest version of QIIME 2 (2024.2). I know condo is installed and updated because when I run conda info --envs, it shows: conda environments: /Users/charlottekunesh/miniconda3 base * /opt/miniconda3 I also have wget, which I know because I am able to run wget --help When I run the first step of the amplicon distribution, I am able to install the file. However when I try to run th…

Good luck!

[Cecile]

Hi @Nicholas_Bokulich,

Thanks for the advice. I have try to remove conda (after ensuring that I am not in a conda environment) using

bash-3.2$ conda deactivate
bash-3.2$ conda remove --all

but I gave an error too...

Error while loading conda entry point: conda-libmamba-solver (dlopen(/opt/miniconda3/lib/python3.9/site-packages/libmambapy/bindings.cpython-39-darwin.so, 0x0002): tried: '/opt/miniconda3/lib/python3.9/site-packages/libmambapy/bindings.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/opt/miniconda3/lib/python3.9/site packages/libmambapy/bindings.cpython-39-darwin.so' (no such file), '/opt/miniconda3/lib/python3.9/site-packages/libmambapy/bindings.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64'))) /opt/miniconda3/lib/python3.9/site-packages/conda_package_streaming/package_streaming.py:25: UserWarning: zstandard could not be imported. Running without .conda support.
warnings.warn("zstandard could not be imported. Running without .conda support.") /opt/miniconda3/lib/python3.9/site-packages/conda_package_handling/api.py:29: UserWarning: Install zstandard Python bindings for .conda support
_warnings.warn("Install zstandard Python bindings for .conda support")
CondaEnvironmentError: cannot remove current environment. deactivate and run conda remove again

[Nicholas_Bokulich]

I believe that conda remove --all is used for removing packages from an existing environment. But I think that your conda might be messed up and you should try uninstalling and re-installing conda if you can. You could also look here for troubleshooting steps (where the final advice was to uninstall, hence where I am getting this from): "Encountered an SSL error" · Issue #13665 · conda/conda · GitHub

This appears to be an issue with conda, not with QIIME 2 per se, so unfortunately I cannot really offer any more insight...

[Cecile]

Thanks, it worked for me.