Hi everyone, hope you are doing fine,
I’m totally new on QIIME2 and I’m trying to import my raw data and I already had some issues.
My data is from the Illumina MiSeq and I believe it’s already demultiplexed, since I only have 2 fastq files per sample (i.e: 19_S19_L001_R1_001.fastq and 19_S19_L001_R2_001.fastq).
This is what I’ve being doing:
(qiime2-2018.8) [email protected]:~$ mkdir sf_qiime2_shared_folder
(qiime2-2018.8) [email protected]:~$ cd sf_qiime2_shared_folder
(qiime2-2018.8) [email protected]:~/sf_qiime2_shared_folder$ qiime tools import \
> --type ‘SampleData[PairedEndSequencesWithQuality]’ \
> --input-path casava \
> --input-format CasavaOneEightSingleLanePerSampleDirFmt \
> --output-path demux-paired-end.qza
I created the shared folder “ qiime2_shared_folder ” and defined it as my directory, and tried to import the folder “casava” (which contains the fastq files for the analysis), however I get the message:
Error: Invalid value for "–input-path": Path "casava" does not exist
And when I give the command ls sf_qiime2_shared_folder , I get the error message:
ls: cannot access ‘sf_qiime2_shared_folder’: No such file or directory
I think I misunderstood the directory function and cannot define it properly (causing the problem to import the files). I believe it’s a very simple step, since it’s the first one, so I’m sorry for the basic question, but if anyone could help me, I would be really grateful.
Thanks in advance!