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_001\.fastq\.gz’`
What other file should I need? I just want to import it make demux summary and procede with deblur.
Thank you so much for any help
Welcome to the forum!
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
Hi @zzkar, if you were able to demultiplex your results into per-sample files, then you could import that and proceed with your analysis.
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