Hi QIIME2 Team,
I am downloading data from nasal samples using q2 fondue and an getting the following error when I get see results from running the search query on the SRA ( human\[All Fields\] AND 16S\[All Fields\] AND nasal\[All Fields\] - BioSample - NCBI )
qiime fondue get-ids-from-query
--p-query '("Homo sapiens"[Organism] OR human[All Fields]) AND 16S[All Fields] AND nasal[All Fields]'
--p-email meghnasw.96@gmail.com
--p-n-jobs 28
--o-ids ids_human_amplicon_nasal2.qza
--verbose
Output:
/opt/conda/envs/fondue/lib/python3.9/site-packages/q2cli/core/cache.py:136: UserWarning: pkg_resources is deprecated as an API. See Package Discovery and Resource Access using pkg_resources - setuptools 80.9.0 documentation . The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
2025-08-11 11:08:29,776 [MainThread] [INFO] [entrezpy.conduit.Conduit]: {"querying": {"queryid": "U4z05fmSRv-cPBww3wfZKQ==", "util": "elink"}}
2025-08-11 11:08:30,778 [MainThread] [INFO] [entrezpy.conduit.Conduit]: {"querying": {"queryid": "y557r6bcTGyzpq8Ba9LHGg==", "util": "efetch"}}
2025-08-11 11:08:32,781 [MainThread] [INFO] [entrezpy.conduit.Conduit]: {"querying": {"queryid": "BozU0QcpQIuoNCaMlBQXLQ==", "util": "elink"}}
2025-08-11 11:08:34,784 [MainThread] [INFO] [entrezpy.conduit.Conduit]: {"querying": {"queryid": "kSXNkdDQQBmYMdwyxwIatQ==", "util": "efetch"}}
2025-08-11 11:08:36,787 [MainThread] [INFO] [entrezpy.conduit.Conduit]: {"querying": {"queryid": "cfJxpqSbQrCJmcPP850XJQ==", "util": "elink"}}
2025-08-11 11:08:38,790 [MainThread] [INFO] [entrezpy.conduit.Conduit]: {"querying": {"queryid": "Etykhpg1Sdy_Ya0EVK0FOw==", "util": "efetch"}}
2025-08-11 11:08:40,794 [MainThread] [INFO] [entrezpy.conduit.Conduit]: {"querying": {"queryid": "X50f_u0jQ7GZ0BdrOJkVPA==", "util": "elink"}}
2025-08-11 11:08:42,797 [MainThread] [INFO] [entrezpy.conduit.Conduit]: {"querying": {"queryid": "n6vCybz3QUe4gVSvUR9JXA==", "util": "efetch"}}
2025-08-11 11:08:43,799 [MainThread] [INFO] [entrezpy.conduit.Conduit]: {"querying": {"queryid": "u9bo5z4WTWONe1iq1IiApw==", "util": "elink"}}
Traceback (most recent call last):
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "", line 2, in get_ids_from_query
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/qiime2/sdk/action.py", line 576, in callable_executor
output_views = self._callable(**view_args)
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/q2_fondue/query.py", line 35, in get_ids_from_query
run_ids = _get_run_ids(
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/q2_fondue/entrezpy_clients/_pipelines.py", line 117, in _get_run_ids
econduit.run(run_ids_pipeline)
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/entrezpy/conduit.py", line 189, in run
Conduit.analyzers[q.id] = self.link(q)
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/entrezpy/conduit.py", line 280, in link
return entrezpy.elink.elinker.Elinker(self.tool,
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/entrezpy/elink/elinker.py", line 75, in inquire
self.request_pool.drain()
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/entrezpy/requester/requestpool.py", line 87, in drain
self.run_single()
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/entrezpy/requester/requestpool.py", line 101, in run_single
analyzer.parse(response, request)
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/entrezpy/base/analyzer.py", line 117, in parse
self.analyze_result(response, request)
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/entrezpy/elink/elink_analyzer.py", line 121, in analyze_result
self.analyze_links(response['linksets'], lset_unit)
File "/opt/conda/envs/fondue/lib/python3.9/site-packages/entrezpy/elink/elink_analyzer.py", line 192, in analyze_links
self.logger.warning(json.dumps({'Empty linkset'}))
File "/opt/conda/envs/fondue/lib/python3.9/json/init.py", line 231, in dumps
return _default_encoder.encode(obj)
File "/opt/conda/envs/fondue/lib/python3.9/json/encoder.py", line 199, in encode
chunks = self.iterencode(o, _one_shot=True)
File "/opt/conda/envs/fondue/lib/python3.9/json/encoder.py", line 257, in iterencode
return _iterencode(o, 0)
File "/opt/conda/envs/fondue/lib/python3.9/json/encoder.py", line 179, in default
raise TypeError(f'Object of type {o.class.name} '
TypeError: Object of type set is not JSON serializable
Plugin error from fondue:
Object of type set is not JSON serializable
See above for debug info.
Thank you for your assistance.
Meghna