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