Manifest.csv is not a(n) PairedEndFastqManifestPhred33 file


I am having trouble importing my fastq file into QIIME2. My manifest file seem to be correct but I have read about invisible things in the file that can affect things and I do not know how to find the invisible characters.

Can someone help me please?

Here is the code I am using:
qiime tools import
–type ‘SampleData[SequencesWithQuality]’
–input-path /igbgroup/n-z/valizad2/Dissertation_Pilot/Microbiome_Analysis/20181012-PrimerSorted-Manifest.csv
–output-path 20181012-single-end-demux.qza
–input-format SingleEndFastqManifestPhred33

and here is the error:

There was a problem importing /igbgroup/n-z/valizad2/Dissertation_Pilot/Microbiome_Analysis/20181012-PrimerSorted-Manifest.csv:

/igbgroup/n-z/valizad2/Dissertation_Pilot/Microbiome_Analysis/20181012-PrimerSorted-Manifest.csv is not a(n) SingleEndFastqManifestPhred33 file

Hey there @Negin! We need a little more information in order to help you — can you please share your manifest? Feel free to send to me in a private message if you need to keep these data private.

Thanks! :t_rex:

Hi Matthew,

Thank you for your reply. I was able to read in the sequences. I was using the wrong method. This is what I used and it worked. I just had to zip my file first. I am just wondering why we can’t use this method for unzipped files because none of the other methods works for me.

qiime tools import \

–type EMPSingleEndSequences \

–input-path /igbgroup/n-z/valizad2/Dissertation_Pilot/Microbiome_Analysis/Sequences/V4_20181012_sequences/ \

–output-path V4-20181012-emp-single-end-sequences.qza

Good to hear! Glad you figured it out!

The only method that works on unzipped FASTQ files are the manifest formats.

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