importing 16s data

Hello,I have download the 16s sequecing data,and split it to two files,
constructed a manifest:
sample-id,absolute-filepath,direction
SRR77013701 $PWD/home/feipang/fastqjoin.un1.fastq.gz,forward
SRR77013701 $PWD/home/feipang/fastqjoin.un1.fastq.gz,forward
import the manifest:qiime tools import \
–type’SampleData [SequencesWithQuality]’ \
–input-path feipang-manifest.txt \
–output-path feipang-demux.qza
–input-format SingleEndFastqManifestPhred33

There were some problems with the command:
(1/4) Missing option “–type”.
(2/4) Missing option “–input-path”.
(3/4) Missing option “–output-path”.
(4/4) Got unexpected extra argument ( )
(qiime2-2019.4) [email protected]:~/Desktop/NGS$ --type’SampleData [SequencesWithQuality]’ \
–typeSampleData [SequencesWithQuality]: command not found
(qiime2-2019.4) [email protected]:~/Desktop/NGS$ --input-path feipang-manifest.txt \
–input-path: command not found
(qiime2-2019.4) [email protected]:~/Desktop/NGS$ --output-path feipang-demux.qza \

–input-format SingleEndFastqManifestPhred33
–output-path: command not found

Thank you

Hi! Maybe its just because of the typo
Instead of:

Try

qiime tools import \
    --type SampleData[SequencesWithQuality] \
    --input-path feipang-manifest.txt \
    --output-path feipang-demux.qza \
    --input-format SingleEndFastqManifestPhred33
1 Like

Thank you!I have changed!
But there have a problem,what is the matter?
(qiime2-2019.4) [email protected]:~/Desktop/NGS$ qiime tools import \

--type SampleData[SequencesWithQuality] \
--input-path manifest.txt \
--output-path feipang-demux.qza \
--input-format SingleEndFastqManifestPhred33

There was a problem importing manifest.txt:

manifest.txt 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’]

Pay closer attention to the error message, each label should be in ‘’, like ‘sample-id’, ‘absolute-filepath’, ‘direction’, not like ‘sample-id,absolute-filepath,direction’. Check you manifest file.

Thanks for pointing that out @timanix. @caidefeng, in case it isn’t clear:

[‘sample-id’, ‘absolute-filepath’, ‘direction’] # this is what _should_ be on the first line
[‘sample-id,absolute-filepath,direction’] # this is what _was found_ on the first line

Thank you very much!
(qiime2-2019.4) [email protected]:~/Desktop/NGS$ qiime tools import
–type SampleData[SequencesWithQuality]
–input-path manifest1.csv
–output-path feipang-demux.qza
–input-format SingleEndFastqManifestPhred33

Imported manifest1.csv as SingleEndFastqManifestPhred33 to feipang-demux.qza

But I have only choose the reverse or forward!I can not choose the reverse and forward at the same time!such as :
manifest contain reverse and forward,
qiime tools import
–type SampleData[SequencesWithQuality]
–input-path manifest1.csv
–output-path feipang-demux.qza
–input-format PairedEndFastqManifestPhred33
there have a problem:
An unexpected error has occurred:

No format: pairleEndFastqManifestPhred33

See above for debug info

Hello @caidefeng!

The error is because this word is misspelled, it should be PairedEndFastqManifestPhred33. Also, in the that case, the type should be SampleData[PairedEndSequencesWithQuality].

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