Need help in importing demultiplexed pair-end data

Hi one and all.

I am new to Qiime2 and I have 16s rRNA fastq files and I am unable to import them successfully.

I made a directory named data1 inside the documents folder/directory of my computer. I put in it my 4 fastq files (my sequences demultiplexed pair-end) and the manifest (tsv) file. My code is the following:

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-format PairedEndFastqManifestPhred33V2
--input-path data1/manifest.tsv
--output-path data1 \

My manifest file content is:
Sample-id forward-absolute-filepath reverse-absolute-filepath
KC $PWD/data1/KC_1.fastq $PWD/data1/KC_2.fastq
FO $PWD/data1/KC_1.fastq $PWD/data1/FO_2.fastq

Please help me. I am using Qiime2 2021.8. Many thanks in advance.


Hi @g.e.wilson,

Without seeing your exact error message I can't say for sure that this is the only issue, but what I'm seeing from your command above is that you've specified the --output-path as data1 instead of something like paired-end-demux.qza. You'll need to specify a path to a file where you'd like this .qza to be written to vs. a directory (since your output will be a single QIIME 2 Artifact, not a directory).

Hope this helps! Cheers :lizard:

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