Dear all,
I have data that was sequenced in multiple runs. With some of the runs, the sequencing center made an error and over-sequenced it (median ~250K reads per sample), while other runs have ~20K per sample.
I want to subsample over-sequenced runs before running dada2.
Issue:
I have freshly installed qiime2-amplicon-2024.10. Data was imported using this version. Then I run the code:
!qiime demux subsample-paired \
--i-sequences {BIGOUT}/{rr}-demux.qza \
--p-fraction {frac} \
--o-subsampled-sequences {BIGOUT}/{rr}-demux_subs.qza
And got the error:
Traceback (most recent call last):
File "/home/ty/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/archive/archiver.py", line 118, in _get_versions
with self.open(self.VERSION_FILE) as fh:
File "/home/ty/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/archive/archiver.py", line 248, in open
return open(os.path.join(self.path, relpath))
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/qiime2/ty/data/57256010-0b6d-4d53-83ec-1db6bf681324/VERSION'During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ty/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/util.py", line 486, in _load_input_file
artifact = qiime2.sdk.Result.load(fp)
File "/home/ty/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/sdk/result.py", line 76, in load
archiver = cache._load_uuid(peek.uuid)
File "/home/ty/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/cache.py", line 1032, in _load_uuid
return Archiver.load_raw(path, self)
File "/home/ty/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/archive/archiver.py", line 385, in load_raw
archive = cls.get_archive(filepath)
File "/home/ty/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/archive/archiver.py", line 320, in get_archive
archive = _NoOpArchive(filepath)
File "/home/ty/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/archive/archiver.py", line 92, in init
self.version, self.framework_version = self._get_versions()
File "/home/ty/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/qiime2/core/archive/archiver.py", line 128, in _get_versions
raise ValueError("Archive does not contain a correctly formatted"
ValueError: Archive does not contain a correctly formatted VERSION file.The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/ty/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/click/type.py", line 118, in _convert_input
result, error = q2cli.util._load_input(value)
File "/home/ty/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/util.py", line 391, in _load_input
artifact, error = _load_input_file(fp)
File "/home/ty/miniconda3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/q2cli/util.py", line 492, in _load_input_file
raise ValueError(
ValueError: It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'SampleData[PairedEndSequencesWithQuality]' and format 'SingleLanePerSamplePairedEndFastqDirFmt'
Then I switched to the qiime2-amplicon-2023.9 version, and run the same command (without reimporting the data), and it worked with no issues:
Saved SampleData[PairedEndSequencesWithQuality] to: /home/ty/Big_data//Limbiom_16S/r9_V12-demux_subs.qza
So the error I am facing only occurred in the latest version of qiime2 (not sure about the 2024.5), but not in the older one (2023.9). I have the workaround but decided to report it here.