version used:
qiime2-2022.2
q2-itsxpress 1.8.0 pypi_0 pypi
itsxpress 1.8.0 pyhdfd78af_2 bioconda
bbmap 38.98 h5c4e2a8_1 bioconda
I was trying to run this command:
qiime itsxpress trim-pair-output-unmerged
--i-per-sample-sequences paired-end-demux.qza
--p-region ITS2
--p-taxa F
--p-threads 4
--o-trimmed trimmed.qza
After an hour or so of running the command, I got the following error:
Plugin error from itsxpress:
/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-y7x6o929/F23_38_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:
Missing sequence for record beginning on line 9
Debug info has been saved to /tmp/qiime2-q2cli-err-jovciu4z.log
Below is what is at the end of the log file
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/plugin/model/file_format.py", line 26, in validate
self._validate_(level)
File "/home/ubuntu/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_types/per_sample_sequences/_format.py", line 284, in _validate_
self._check_n_records(record_count_map[level])
File "/home/ubuntu/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_types/per_sample_sequences/_format.py", line 253, in _check_n_records
raise ValidationError('Missing sequence for record '
qiime2.core.exceptions.ValidationError: Missing sequence for record beginning on line 9
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
results = action(**arguments)
File "<decorator-gen-461>", line 2, in trim_pair_output_unmerged
File "/home/ubuntu/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self._callable_executor_(scope, callable_args,
File "/home/ubuntu/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 418, in _callable_executor_
artifact = qiime2.sdk.Artifact._from_view(
File "/home/ubuntu/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/result.py", line 305, in _from_view
result = transformation(view, validate_level)
File "/home/ubuntu/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/core/transform.py", line 68, in transformation
self.validate(view, level=validate_level)
File "/home/ubuntu/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/core/transform.py", line 143, in validate
view.validate(level)
File "/home/ubuntu/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/plugin/model/directory_format.py", line 173, in validate
getattr(self, field)._validate_members(collected_paths, level)
File "/home/ubuntu/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/plugin/model/directory_format.py", line 103, in _validate_members
self.format(path, mode='r').validate(level)
File "/home/ubuntu/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/plugin/model/file_format.py", line 28, in validate
raise ValidationError(
qiime2.core.exceptions.ValidationError: /tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-y7x6o929/F23_38_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:
Missing sequence for record beginning on line 9
``
The log file attached as well.
I checked the sequencing file for the error on line 9, but it looks OK to me!
Any help to navigate through this error is highly appreciated!
Thanks in advance.
Aseeri
