QIIME2 not detecting reverse reads from menifest file


I have been trying to import my paired end files in QIIME2 but each time it displays following error for all my files:

"forward and reverse reads must be provided one time each for each sample. The following samples had forward reads but not reverse reads":

I have attached the menifest file and an image of the error kindly help me in this regard.

Best regards,

Faizan Saleem

Menifest_file.csv (4.7 KB)

1 Like

Hello Faizan,

Thank you for posting your manifest file. I think you are on the right track and a small update to the manifest file will make this script work for you.

When I look at your file, I see this:

sample-id absolute-filepath direction
BN-1_1.fq.gz /home/faizansaleem/Desktop/faizan/Betel-Nut_Data forward
BN-1_2.fq.gz /home/faizansaleem/Desktop/faizan/Betel-Nut_Data reverse
BN-2_1.fq.gz /home/faizansaleem/Desktop/faizan/Betel-Nut_Data forward
BN-2_2.fq.gz /home/faizansaleem/Desktop/faizan/Betel-Nut_Data reverse

Note how your absolute-filepath column is always the same! That’s wont work.

Try reformatting your file like this:

sample-id absolute-filepath direction
BN-1 /home/faizansaleem/Desktop/faizan/Betel-Nut_Data/BN-1_1.fq.gz forward
BN-1 /home/faizansaleem/Desktop/faizan/Betel-Nut_Data/BN-1_2.fq.gz reverse
BN-2 /home/faizansaleem/Desktop/faizan/Betel-Nut_Data/BN-2_1.fq.gz forward
BN-2 /home/faizansaleem/Desktop/faizan/Betel-Nut_Data/BN-2_2.fq.gz reverse

Let me know if this reformatting works for you.


P.S. There are more details about this file format on this page.


Dear Colin thanks a lot for a swift reply. Yeah I noticed it yesterday and made the adjustments in file. It worked like a charm.

Faizan Saleem


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