Samples missing BioProjectID: fondue error
Dear QIIME2 Team,
I am trying to download fecal samples from fondue using the folowing commands and get the following error. I am using qiime2-amplicon-2024.10 version.
Thanks for your help in advance!
Meghna
qiime fondue get-ids-from-query
--p-query '("Homo sapiens"[Organism] OR human[All Fields]) AND 16S[All Fields] AND healthy[All Fields] AND (feces[All Fields] OR fecal[All Fields]) NOT child[All Fields]'
--p-email meghnasw.96@gmail.com
--p-n-jobs 28
--o-ids ids_human_amplicon_fecal.qza
--verbose
qiime fondue get-metadata
--i-accession-ids ids_human_amplicon_fecal.qza
--p-n-jobs 24
--p-email ‘myemail.com’
--output-dir human_fecal_metadata
--verbose 2>&1
| tee fondue_get-metadata_fecal.log
ERROR:
2025-11-17 15:07:35,991 [MainThread] [INFO] [q2_fondue.metadata]: Fetching metadata for 1884 run IDs.
/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_fondue/entrezpy_clients/_efetch.py:69: FutureWarning: DataFrame.groupby with axis=1 is deprecated. Do `frame.T.groupby(...)` without axis instead.
df = df.groupby(level=0, axis=1).first()
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/plugin/model/file_format.py", line 26, in validate
self.\_validate\_(level)
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_fondue/types/_format.py", line 51, in _validate_
self.\_validate()
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2_fondue/types/_format.py", line 45, in _validate
raise ValidationError(
qiime2.core.exceptions.ValidationError: Some samples are missing IDs in the following fields: Bioproject ID.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/commands.py", line 530, in _call_
results = self.\_execute_action(
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/commands.py", line 602, in _execute_action
results = action(\*\*arguments)
File "", line 2, in get_metadata
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 299, in bound_callable
outputs = self.\_callable_executor\_(
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 587, in _callable_executor_
self.signature.coerce_given_outputs(output_views, output_types,
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/type/signature.py", line 498, in coerce_given_outputs
output = self.\_create_output_artifact(
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/type/signature.py", line 520, in _create_output_artifact
artifact = qiime2.sdk.Artifact.\_from_view(
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/result.py", line 374, in _from_view
result = transformation(view, validate_level)
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/transform.py", line 224, in wrapped
new_view.file.write_data(file_view, self.\_wrapped_view_type)
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/plugin/model/directory_format.py", line 92, in write_data
result = transformation(view)
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/transform.py", line 68, in transformation
self.validate(view, level=validate_level)
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/transform.py", line 143, in validate
view.validate(level)
File "/home/ubuntu/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/plugin/model/file_format.py", line 28, in validate
raise ValidationError(
qiime2.core.exceptions.ValidationError: /tmp/qiime2/ubuntu/processes/135235-1763392044.93@ubuntu/tmp/q2-OutPath-dpe_h1kq is not a(n) SRAMetadataFormat file:
Some samples are missing IDs in the following fields: Bioproject ID.
Plugin error from fondue:
/tmp/qiime2/ubuntu/processes/135235-1763392044.93@ubuntu/tmp/q2-OutPath-dpe_h1kq is not a(n) SRAMetadataFormat file:
Some samples are missing IDs in the following fields: Bioproject ID.