importare file casava 1.8

User Support
1

Hello everyone,
I have a problem with importing my data.
here is the format of my data:
Fen-Bac-KKT10.R1.fastq.gz Fen-Bac-KKT10.R2.fastq.gz

Here is the command I use:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /galileo/home/userexternal/jdimarti/CINECA_SCRATCH/microbio_mari/gorrasi
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path demux-paired-end.qza

unfortunately I get an error:
There was a problem importing /galileo/home/userexternal/jdimarti/CINECA_SCRATCH/microbio_mari/gorrasi:

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

Could someone tell me where am i wrong?
Thanks :slight_smile:

2

Hi @jessidima,

I suspect using the '--input-format CasavaOneEightSingleLanePerSampleDirFmt', qime2 expects the file names still as output of the casava demultiplexing step, something like sample_L000_R1_001.fastq.gz. It seems that your files have been renamed and so qiime2 can not find any casava file in the folder you pointing at.
You can either rename them to restore the original format or try to use a manifest file to import them, you can find more info in the import tutorial: Importing data — QIIME 2 2020.8.0 documentation

Hope it helps
Luca