I'm currently trying to import a set of paired-end demultiplexed reads using the manifest format, and for some reason it's not working!
Here's my code:
qiime tools import \
--type 'SampleData[SequencesWithQuality]' \
--input-path post_qiita_hackflex_manifest.txt \
--output-path imported_sequences_qiita.qza \
And I get this error:
**There was a problem importing post_qiita_hackflex_manifest.txt:**
**post_qiita_hackflex_manifest.txt is not a directory.**
I'm confused because I know the file exists, and I'm doing everything in the correct directory. My manifest file is attached below.
Thanks for your help!
post_qiita_hackflex_manifest.txt (10.3 KB)
The reason is that you should use "SingleEndFastqManifestPhred33V2" instead of "SingleLanePerSamplePairedEndFastqDirFmt" when importing with a manifest file.
Please, double check that you want to import it as single end reads, cause in your ḿanifest file there are both F and R reads. For paired reads, use "PairedEndFastqManifestPhred64V2".
Thanks for the reply! I had tried PairedEndFastqManifestPhred64V2 earlier, and got this error:
**An unexpected error has occurred:**
**No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred64V2'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>**
**See above for debug info.**
That's why I tried using SingleLanePerSamplePairedEndFastqDirFmt.
for importing paired end reads
Thanks for the suggestion, but I get a similar error to when I try the Phred64V2 offset.
Traceback (most recent call last):
File "/programs/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 157, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/programs/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/result.py", line 240, in import_data
return cls._from_view(type_, view, view_type, provenance_capture,
File "/programs/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/result.py", line 265, in _from_view
transformation = from_type.make_transformation(to_type,
File "/programs/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/core/transform.py", line 58, in make_transformation
raise Exception("No transformation from %r to %r" %
Exception: No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33V2'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>
An unexpected error has occurred:
No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33V2'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>
See above for debug info.
In addition to suggested above variant by @kindergarten, could you also try to change "type"?
This worked! Thanks to both you and @kindergarten!
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