importing demultiplexed fastq.gz files without barcode identifier in filenames

Technical Support
1

Hi all,

I have what I am pretty sure are casava paired end files that are named as such:

F53-Mouflon-R2_RUN2_L1.fastq.gz
F66-Wild-Boar_R1_RUN2_L1.fastq.gz
F66-Wild-Boar_R2_RUN2_L1.fastq.gz
F68-Red-Deer_R1_RUN2_L1.fastq.gz
F68-Red-Deer_R2_RUN2_L1.fastq.gz
F69-Red-Deer_R1_RUN2_L1.fastq.gz
F69-Red-Deer_R2_RUN2_L1.fastq.gz
F70-Red-Deer_R1_RUN2_L1.fastq.gz
F70-Red-Deer_R2_RUN2_L1.fastq.gz
F80-Red-Deer_R1_RUN2_L1.fastq.gz
F80-Red-Deer_R2_RUN2_L1.fastq.gz
F90-Domestic-Dog_R1_RUN2_L1.fastq.gz
F90-Domestic-Dog_R2_RUN2_L1.fastq.gz

When I try to import using:

  qiime tools import \

–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path fastq
–input-format CasavaOneEightSingleLanePerSampleDirFmt
–output-path demux-paired-end.qza

I get the error:

There was a problem importing fastq:

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

I am pretty sure the files are missing the barcode identifiers and am wondering if there is a workaround or do I need to contact the authors in getting the barcode identifiers (its from a public database).

Any help would be appreciated!
Thanks,
Sam

2

This is because that format has a specific naming schema, as outlined here.

Also, see:

3

Hi Mike,

Thanks for the link to the related question. I will try the manifest format and see how that goes.
Thank you
Sam

4

Also this might be the tiniest of details but the example manifest file in the qiime tutorial reads as such:

sample-id	absolute-filepath
sample.1	$PWD/se-33/sample1.fastq.gz
sample2	$PWD/se-33/sample2_S1_L001_R1_001.fastq.gz

And I am not sure if sample.1 is written with the period intended or if that is a mistake. Just wanted to make you guys aware just in case it is a mistake

5

Good eye @Sam_Degregori, this is just to highlight the acceptable sample-id formats. You can check out the Recommendations for Identifiers documentation for more details.

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6

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