Error importing reads

Hi my reads folder has three files: Raw_Read1.fq.gz, Raw_Read3.fq.gz and Raw_Read2_Barcodes.fq.gz
and running this command:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path reads
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path demux-paired-end.qza

This is not working. I am getting following error while importing reads.
There was a problem importing reads:

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

Please guide.

Thank you!

I have just figured out this.
Perhaps it's because the file name, you should make them as 'sampleID_BarcodeIndex_LANENUM_R[1/2]_001.fastq.gz’
Try to see if it works or not.


1 Like

Thank you for your reply. Just wanted to confirm, out of three files i have: Raw_Read1.fq.gz, Raw_Read3.fq.gz and Raw_Read2_Barcodes.fq.gz

I should only relabel Raw_Read2_Barcodes.fq.gz as sampleID_BarcodeIndex_LANENUM_R[1/2]_001.fastq.gz ? What about the other two files? Please let me know


Since your file naming does not follow the standard Casava convention and you have a barcodes file, your data is not Casava formatted. I think you might be better off using a manifest import as described here.

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