qiime tools import error for paired end reads

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path $data_to_import
--output-path demultiplexed-sequences.qza
There was a problem importing /media/mo/New_Volume/16S/samples:

Missing one or more files for SingleLanePerSamplePairedEndFastqDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz'

Hi @Mohamed_S.AboHoussie :smiley: :wave:

What is this variable "$data_to_import"? A bit more infromation when asking questions on the forum will make it easier for people to help you and get to the bottom of the issue.
It looks like you are trying to import your paired end data using the format where it's expected to have reads that have a format similar to this:


It doesn't appear that your data has that format (lane number, and read direction included). I would just make an import manifest, which is a tab serperated file to tell qiime2 where to find your reads using absolute paths.

This importing tutorial covers all types of data and methods to import them.

all the best,



Hello Vic,
I'm glad to your kindly response
The variable contains the absolute path for my samples

So it's ends to all samples.

I will try the manifest solution.

Mohamed AboHoussien

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Hi @Mohamed_S.AboHoussie,
I agree with @buzic, using a manifest is your most effective option!


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Looks like that file is comma-separated, even though it's extension is .tsv.
Screenshot 2024-02-19 at 10.32.31 PM

Save it as a tab-separated file and try again!

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I have 400 samples so I can't make the manifest manually is there is any script to do it ??

Hi again @Mohamed_S.AboHoussie,

I am unaware of any Qiime2 script to make manifests.

Unfortunately, I think this is where learning some basic coding comes in. I have written my own Python scripts to make my manifests when datasets are large and this is probably your best bet. If you are more proficient in R then obviously would use that.

Alternatively, you could searching the forum for "make manifest" as some people have shared their code, for example here, here or here.

best of luck!


An off-topic reply has been split into a new topic: Taxa filter-table: All Features must be in the taxonomy

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Hello Mohamed,

You don't have to make a new manifest file, you have one that looks good!

The only problem is the format. Once you save it using the correct format in LibreOffice, this problem should be resolved.


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