Hi @Keegan-Evans. Thank you for your reply. It seems working now.
The full output of the error was as below. It seems like something went wrong with the UTF-8:
Unexpected error importing data:
/mnt/efs/fs1/cancer-usegalaxy-shared/
database/datasets/062/dataset_62177.d
at is not a(n)
SingleEndFastqManifestPhred33V2 file:
Metadata file must be encoded as
UTF-8 or ASCII. The following error
occurred when decoding the file:
'utf-8' codec can't decode byte 0x8b
in position 1: invalid start byte
There may be more errors present in
the metadata file. To get a full
report, sample/feature metadata files
can be validated with Keemei:
https://keemei.qiime2.org
Find details on QIIME 2 metadata
requirements here: https://docs.qiime
2.org/2022.11/tutorials/metadata/
:(
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/metadata/io.py", line 73, in read
header = self._read_header()
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/metadata/io.py", line 145, in _read_header
for row in self._reader:
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/metadata/io.py", line 71, in <genexpr>
self._reader = (self._strip_cell_whitespace(row)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/encodings/utf_8_sig.py", line 69, in _buffer_decode
return codecs.utf_8_decode(input, errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2_types/per_sample_sequences/_format.py", line 40, in _validate_
md = qiime2.Metadata.load(str(self))
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/metadata/metadata.py", line 396, in load
return MetadataReader(filepath).read(
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/metadata/io.py", line 84, in read
raise MetadataFileError(
qiime2.metadata.io.MetadataFileError: Metadata file must be encoded as UTF-8 or ASCII. The following error occurred when decoding the file:
'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org
Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2022.11/tutorials/metadata/
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/plugin/model/file_format.py", line 26, in validate
self._validate_(level)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2_types/per_sample_sequences/_format.py", line 42, in _validate_
raise ValidationError(md_exc) from md_exc
qiime2.core.exceptions.ValidationError: Metadata file must be encoded as UTF-8 or ASCII. The following error occurred when decoding the file:
'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org
Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2022.11/tutorials/metadata/
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2022.11/bin/q2galaxy", line 11, in <module>
sys.exit(root())
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2galaxy/__main__.py", line 96, in run
builtin_runner(action, config)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2galaxy/core/drivers/builtins.py", line 24, in builtin_runner
tool(inputs, stdio=stdio)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2galaxy/core/drivers/builtins.py", line 43, in import_data
artifact = _import_name_data(type_, format_, files_to_move,
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2galaxy/core/drivers/stdio.py", line 38, in wrapped
return function(*args, **kwargs)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/q2galaxy/core/drivers/builtins.py", line 79, in _import_name_data
return qiime2.Artifact.import_data(type_, path, view_type=format_)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/result.py", line 321, in import_data
return cls._from_view(type_, view, view_type, provenance_capture,
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/sdk/result.py", line 349, in _from_view
result = transformation(view, validate_level)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/core/transform.py", line 68, in transformation
self.validate(view, level=validate_level)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/core/transform.py", line 143, in validate
view.validate(level)
File "/opt/conda/envs/qiime2-2022.11/lib/python3.8/site-packages/qiime2/plugin/model/file_format.py", line 28, in validate
raise ValidationError(
qiime2.core.exceptions.ValidationError: /mnt/efs/fs1/cancer-usegalaxy-shared/database/datasets/062/dataset_62177.dat is not a(n) SingleEndFastqManifestPhred33V2 file:
Metadata file must be encoded as UTF-8 or ASCII. The following error occurred when decoding the file:
'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org
Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2022.11/tutorials/metadata/
After following your instruction, I successfully imported the FASTQ.GZ files. I still have one more question.
In your screenshot, there's an 'Add Elements' section where you specified the name as 'sampleID_barcode1_R1_001.fastq.gz'. However, the sample names in my case (IBD177, IBD178) and their corresponding URLs do not adhere to that particular format. Despite the discrepancy between the sample's name and the specified rules, I proceeded with the input based on your screenshot. What would be the correct approach in this situation?