casava 1.8 paired end importing error

Hi Qiime team, I am an undergrad working on a comparative microbiome research project with @Sam_Degregori. I am importing casava 1.8 paired-end files formatted as so:


However, I keep getting this error.

qiime tools import \

--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path zoelzer
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path zoelzercpative-demux-paired-end.qza

There was a problem importing zoelzer:

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

Is there a way to rename my files to match the required format for Casava 1.8? I know I can manifest these, but because of the metadata we have at hand, it would be much easier to import the Casava way. When we manifest it, the sample IDs are nonexistent and we would have to make up our own, but if we use Casava we know the file names are in the fastq.gz files. Any help would be appreciated it! Thank you!


You certainly can manually change the names on your file to match the CASAVA convention: L2S357_15_L001_R2_001.fastq.gz, where the first position is your sampleID, the next does not particularly matter, the third being the lane and must follow the format of a capital 'L' followed by 3 numbers, the fourth being the read direction(R1 for forward and R2 for reverse), with 001 following the final underscore.

Ultimately it might still be easier to generate a barcodes file, import using manifest, and then demultiplex using the appropriate cutadapt demux function.

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