Unrecognized files for Casava 1.8 paired-end demultiplexed fastq

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1

Hey, I'm facing a problem importing my data into QIIME 2 with Casava 1.8 single-end demultiplexed FASTQ files. I'm receiving the following message:

"There was a problem importing /home/zineb/analysis/seqs:

Unrecognized file (/home/zineb/analysis/seqs/SRR7637842_RR3_L001_R1_003.fastq.gz) for CasavaOneEightSingleLanePerSampleDirFmt."

Those are my files, and this is the command I used to import:

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /home/zineb/analysis/seqs --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path /home/zineb/analysis/combined.qza"
SRR7637842_RR3_L001_R1_003.fastq.gz
SRR7637842_RR3_L001_R2_003.fastq.gz
SRR7637844_RR5_L001_R1_005.fastq.gz
SRR7637844_RR5_L001_R2_005.fastq.gz
SRR7637845_RR6_L001_R1_006.fastq.gz
SRR7637845_RR6_L001_R2_006.fastq.gz
SRR7637846_RR1_L001_R1_001.fastq.gz
SRR7637846_RR1_L001_R2_001.fastq.gz
SRR7637847_RR2_L001_R1_002.fastq.gz
SRR7637847_RR2_L001_R2_002.fastq.gz
and thank you.

2

Hi @Zineb,
Casava format is very particular.
I am not exactly sure whats wrong off the bat. I have never seen a value for the set under that isn't the 001. ex: SRR7637842_RR3_L001_R1_003.fastq.gz. Maybe that is the reason? You could try editing your file names to have 001? But I am not sure that is the issue.

Could you send me a screenshot of the output of ls /home/zineb/analysis/seqs?

3

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