Problem importing SAMPLE is not a(n) FastqGzFormat file: Missing sequence for record beginning on line 33313

Hi all!

I am using QIIME2 version 2021.2. I amtrying to import some 16S paired end data using the following command:

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path Seqs --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path paired-end-demux-seqs.qza

But I am having this problem:

There was a problem importing Seqs: Seqs/81_S3_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file: Missing sequence for record beginning on line 33313

I tried to remove that sample, but that error kept showing, with a different sample each time. I don't want to loose more samples :frowning_face:

Maybe I am doing something wrong, but have no clue. I would really appreciate any help!

Hello again Nickole,

I wonder if this is an issue with how cutadapt processed the sequences for demultiplexing. Perhaps it choose to output reads with zero base-pairs, leading to this error.

Could you post the full cutadapt command you ran outside of Qiime2 so we can take a look?

x-ref to last post about demultiplexing these strange reads :face_with_monocle: