I am trying to import my data to qiime2, I followed the tutorial of imparting data, my data is paired end and already demultiplexed as the data received from sequencing center have two files for each sample one for forward reads and the another for reverse, the header of one file as shown below,
so I used the command
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path My-data-single-end-demultiplexed
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path demux-paired-end.qza
however I got this error
The error is highlighting that the names of the files do not comply with the Casava naming format.
I would suggest making a Manifest file and import that way.
Hi @SoilRotifer
sorry for that but I tried many times with Manifest file importing and got an error as well
Manifest file was created and saved as .tsv extension
the following command was used
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path pe-33-manifest
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2
however, I got this error
when I used the list command all required files are in the same path
The OS can visually "hide" the extensions like .tsv etc in the GUI interface. But in the command line you have to provide the full file name. In your directory list you can see the file is indeed pe-33-manifest.tsv, but your qiime command only contained pe-33-manifest.
!
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