Error with qiime tools import_import does not recognize Casava format

[manoch (Manuel Ochoa)]

Hi all!

I am trying to import fastq.gz paired end files without manifest file in qiime 2. I am using the following code:

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /home/manuel_os/bird2 --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza

But the following error appears:

There was a problem importing /home/manuel_os/bird:

/home/manuel_os/penguin is not a(n) CasavaOneEightSingleLanePerSampleDirFmt:

Duplicate samples in forward reads: {'S_mage_back', 'S_mage_plum', 'A_pata_back', 'S_mage_foot', 'S_mage_nest', 'A_pata_plum', 'A_pata_foot'}

Here is an example of the name of my files:

A_pata_back_1_L001_R1_001.fastq.gz
A_pata_back_1_L001_R2_001.fastq.gz

Thanks in advance!

Best regards

[SoilRotifer (Mike Robeson)]

Hi @manoch, welcome to !

This issue is outlined here:

Input Error Assistance

Hi @Megan_Whisonant welcome to ! This issue is that the sequence file names violate the CASAVA naming schema as outlined here. I'd recommend using the Manifest format. See these related posts: -Mik

[manoch (Manuel Ochoa)]

Hi SoilRotifer

I see! Thanks for the feedback and the fast reply!

Excellent day