Hi,
I am trying to import data from this Qiita project https://qiita.ucsd.edu/study/description/11052# to a Qiime artifact. I am working on qiime 2 2020.8. I have downloaded preprocessed.fastq.gz file from demultiplexed step and now I an trying to import it.
I am doing this
!qiime tools import \ --type SampleData[SequencesWithQuality] \ --input-path data \ #here I have my ONE fastq.gz file --output-path emp-single-end-sequences.qza
but I am getting an error
`There was a problem importing data:
Missing one or more files for SingleLanePerSampleSingleEndFastqDirFmt: ‘.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz’`
What other file should I need? I just want to import it make demux summary and procede with deblur.
It looks like by default, when import type for SampleData[SequencesWithQuality] is based on Casava. I would try a manifest format. Have you checked out our fabulous data importing tutorial for all your manifest building needs?
Thank you for the answer @jwdebelius! Unfortunately I think that manifest will not be suitable here as I have only one fastq.gz file. it looks like this
@11052.1.10.14.rk.t_8590 orig_bc=ACTTAGCTTGCA new_bc=ACTTAGCTTGCA bc_diffs=0 TACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTAATAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGTTAAACTTGAGTG + BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFBF/BFFFFFFFFFFFFFFBFF/FFF< @11052.1.10.14.rk.t_8591 orig_bc=ACTTAGCTTGCA new_bc=ACTTAGCTTGCA bc_diffs=0 TACGGAAGGTCAGGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCCGTTTGATAAGCGTGCTGTGAAATATAGTGGCTCAACCTCTATCGTGCAGCGCGAACTGTTGAACTTGAGTGC +
What I did I demutliplexed this file using BBMAP demultiplexbyname.sh (as barcodes are in headers not in sequences) and imported it to Qiime with a manifest. It worked, I could proceed with my analysis. Do you think that was the right way to do it? I am still a bit unsure
forum!