I am currently trying to import my Casava 1.8 paired-end demultiplexed fastq data I have received from a download on Illumina Basespace into qiime 2 version 2-2021.4 in a conda MacOS environment. However, I am unsure of the language I need to be using. I am trying to import the whole folder, but I am not sure what text to change in my import template that was provided by Qiime 2 docs online. This is the code I ran:
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /Users/SoilMicrobiologyWSU/Nick/M06339_Run131_Neely_MS3064010-242560318/FASTQ_Generation_2021-04-04_08_49_18Z-398026631 --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza
There was a problem importing /Users/SoilMicrobiologyWSU/Nick/M06339_Run131_Neely_MS3064010-242560318/FASTQ_Generation_2021-04-04_08_49_18Z-398026631: Unrecognized file (/Users/SoilMicrobiologyWSU/Nick/M06339_Run131_Neely_MS3064010-242560318/FASTQ_Generation_2021-04-04_08_49_18Z-398026631/B4_ITS2_L001-ds.73754145408645b6bd9901fe7f209eae/B4-ITS2_S326_L001_R1_001.fastq) for CasavaOneEightSingleLanePerSampleDirFmt.
I tried modifying the Casava line to change the text to represent my data but it did not like that either. I am also trying to copy over the entire folder with my 16S and ITS data files. Is this the correct thing to do or do i need to import every individual file with the format similar to this sample id, absolute path, direction? I am very new to python/Qiime and have reviewed tutorials online but am still unsure of where to modify template code. Any help or resources would be appreciated. Thank you!