data import bcl2fastq demultiplexed paired end


Thanks for useful suggestions ahead!

I’m now writing because I tried and input data from an old qiime1 processed dataset, by means of importing fasta, that was OK till abundance abd diversity analyses.

I’m now desiring to input fastq.gz data obtained from Illumina Miseq, already demultiplexed using bcl2fastq, I have tried following the tutorial also including a manifest file, but in the end I was not successful:

qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path manifest/
–output-path demux-paired-end.qza

in the manifest folder i put amanifest.csv, like the following:


It seems there is a problem:

There was a problem importing manifest/:

Missing one or more files for SingleLanePerSamplePairedEndFastqDirFmt: 'MANIFEST

Could you please help me to solve?

I’m running qiime2-2019.10 on a personal Mac for testing.

Morevover could I use just a subsampled file, obtained like this:
seqtk sample -s100 EC1_R1.sample.fastq 10000 > sub1.fq
and similarly for read2?

Thanks a lot


Hi @MichelaRiba,

Great idea! Testing on a subset of your data would be a good way to quickly get things working.

It looks like the issue may be that you are pointing at a directory path, rather than a file path. This line should point to manifest.csv (or whatever you are calling it) instead of the directory path:

Let me know if that helps!

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