I can't import my demultiplexed paired end files


I have paired end demultiplexed files and I am using the following code:

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /gpfs_home/fastq --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path /gpfs_home/demux-paired-end.qza

My files looks like this


with a different made up barcode number for each pair. For example:


List goes on.

I’ve read the other responses to questions like this, but I can’t seem to figure out why I’m still getting the same error message.

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

Hi @Biancabrown! Thanks for the detailed post explaining your problem!

The issue here is that the CasavaOneEightSingleLanePerSampleDirFmt is expecting gzipped fastq files (e.g. foo.fastq.gz), but you are providing non-gzipped files (e.g. foo.fastq).

I think you have two options:

  • gzip all of your files (one-by-one) - we don’t have a utility for that, so you will need to consult your favorite search engine.
  • Use a Manifest format! This format is able to gzip unzipped files while importing. The downside here is you need to create a new file (the manifest), which can be tedious.

Good luck, and let us know if you get stuck! :t_rex:

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Hi @thermokarst

Thanks again, you hit the nail right on the head! This suggestion also worked well.

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