I am trying to do my first import of fastq files into Qiime2 and keep getting the error that the path to the manifest file does not exist. Because I am used to working with windows, I'm wondering if I am misunderstanding the directories in Qiime2. If I make a directory in Qiime2 with the same name as on my hard-drive where the data is, will Qiime2 access my hard-drive or will the directory I made in Qiime2 only be useable within the Qiime2 environment? If the latter, how do I tell Qiime2 where the data is?
First, you are trying to import your fastq and manifest files: in the input-path parameter, you should include the absolute directory path to the q_trimmed_seqs folder (without enter inside the folder), that would avoid problems (you can use the cd command to enter in the folder and the pwd in the terminal to find out what is your absolute directory path). And also, the fastq files should be in a compress form as fastq.gz files.