manifest.list problem to recognize forward-absolute-filepath

[Manuela_Ramalho]

Hi,

I have never imported the sequences with manifest.list and I am having difficulties. I would appreciate any help here.

I'm important with the following command:

qiime tools import
--type 'SampleData[SequencesWithQuality]'
--input-format SingleEndFastqManifestPhred33V2
--input-path manifest.list.txt
--output-path single-end-demux.qza \

And this error appears:
There was a problem importing manifest.list.txt:

manifest.list.txt is not a(n) SingleEndFastqManifestPhred33V2 file:

'absolute-filepath' is not a column in the metadata. Available columns: 'forward-absolute-filepath', 'reverse-absolute-filepath'

However, my manifest.list.txt (separated by tab) contains this column. See below:

sample-id forward-absolute-filepath reverse-absolute-filepath
C1 FDMP170044433-1A_L1_C1.raw_1.fq.gz FDMP170044433-1A_L1_C1.raw_2.fq.gz

Any tips would be very welcome!

Thank you in advance,
Manu

[cherman2 (Chloe Herman)]

Hi @Manuela_Ramalho,

Looks like you are importing this data a SingleEndFastqManifestPhred33V2 but you have paired end data. Try PairedEndFastqManifestPhred33V2, that should work for you!

[Manuela_Ramalho]

Hi Cherman2!

Thank you! I missed this!

Now I found another problem. if you have any additional suggestions I would appreciate too! See below

qiime tools import
--type 'SampleData[SequencesWithQuality]'
--input-format PairedEndFastqManifestPhred33V2
--input-path manifest.txt
--output-path single-end-demux.qza \

Traceback (most recent call last):
File "/Users/manuelaramalho/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 157, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/Users/manuelaramalho/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/result.py", line 299, in import_data
return cls.from_view(type, view, view_type, provenance_capture,
File "/Users/manuelaramalho/miniconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/result.py", line 325, in _from_view
transformation = from_type.make_transformation(to_type,
File "/Users/manuelaramalho/miniconda3/envs/qiime2-2022.8/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.

Again, thank you!!!!

All the best,
Manu

[buzic (Victoria)]

HI @Manuela_Ramalho

I think it might be that you just need to specify paired end in the type option. i.e:

--type 'SampleData[PairedEndSequencesWithQuality]

as at the moment you have the type option as:

--type 'SampleData[SequencesWithQuality]'

Which I think might be for single end.

best,

Vic