importing single-end sequence data

Good day, I am trying to import my sequence data into qiime2 for analysis using manifest using the following command, however i got this error.
(qiime2-2021.11) [email protected]:/media/sf_Qiime2$ qiime tools import \

--type 'SampleData[SequencesWithQuality]'
--input-path manifest.csv
--output-path single-end-demux.qza
--input-format SingleEndFastqManifestPhred33
There was a problem importing manifest.csv:
manifest.csv is not a(n) SingleEndFastqManifestPhred33 file:

Found header on line 1 with the following labels: ['sample-id', '"absolute-filepath', '"', 'direction'], expected: ['sample-id', 'absolute-filepath', 'direction']
Attached are the sample of my sequence and manifest file. I tried to find similar issue in the forum but i could not get, your help will be highly apprecated

Hello @Zango,

I think I found the error!

Note that the expected column is
absolute-filepath
but you have
absolute-filepath, (with a comma at the end.

Fix that column by removing that comma, and try importing again!

2 Likes

Thank you for your reply Sir, I removed the , sign and tried again but i encountered another error again.
(qiime2-2021.11) [email protected]:/media/sf_Qiime2$ qiime tools import \

--type 'SampleData[SequencesWithQuality]'
--input-path manifest.csv
--output-path single-end-demux.qza
--input-format SingleEndFastqManifestPhred33
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 157, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/result.py", line 277, in import_data
return cls.from_view(type, view, view_type, provenance_capture,
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/result.py", line 305, in _from_view
result = transformation(view, validate_level)
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_types/per_sample_sequences/_transformer.py", line 153, in _6
return _fastq_manifest_helper_partial(fmt, _copy_with_compression,
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_types/per_sample_sequences/_util.py", line 233, in _fastq_manifest_helper
input_manifest = _parse_and_validate_manifest(
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_types/per_sample_sequences/_util.py", line 94, in _parse_and_validate_manifest
_validate_header(manifest, expected_header)
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_types/per_sample_sequences/_util.py", line 132, in _validate_header
raise ValueError('Expected manifest header %r but '
ValueError: Expected manifest header 'sample-id,absolute-filepath,direction' but found 'sample-id,absolute-filepath,direction '.

An unexpected error has occurred:

Expected manifest header 'sample-id,absolute-filepath,direction' but found 'sample-id,absolute-filepath,direction '.

See above for debug info.

I have just imported the file, i sorted out the issue with my manifest file. Thank you for your help

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