importing 16s data

[caidefeng (Defeng Cai)]

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) qiime2@qiime2core2019-4:~/Desktop/NGS$ --type'SampleData [SequencesWithQuality]' \
--typeSampleData [SequencesWithQuality]: command not found
(qiime2-2019.4) qiime2@qiime2core2019-4:~/Desktop/NGS$ --input-path feipang-manifest.txt \
--input-path: command not found
(qiime2-2019.4) qiime2@qiime2core2019-4:~/Desktop/NGS$ --output-path feipang-demux.qza \

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

Thank you

[timanix (Timur Yergaliyev)]

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

@caidefeng

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

Try

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

[caidefeng (Defeng Cai)]

Thank you！I have changed！
But there have a problem，what is the matter？
(qiime2-2019.4) qiime2@qiime2core2019-4:~/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']

[timanix (Timur Yergaliyev)]

@caidefeng

[‘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.

[thermokarst]

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

[caidefeng (Defeng Cai)]

Thank you very much！
(qiime2-2019.4) qiime2@qiime2core2019-4:~/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

[thermokarst]

Hello @caidefeng!

@caidefeng

No format: pairleEndFastqManifestPhred33

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