Difficulty importing manifest file into qiime2

I have looked up answers to my particular question on this forum and others but I haven't yet been able to find an answer.

I am very new to bioinformatics in general, and qiime2 is no exception. I am trying to import my already demultiplexed fastq files from my 16S community sequencing run using an Oxford Nanopore Sequencer in order to analyze them and one day dive into metagenomics with them. I have 12 samples (all in separate folders), all with at least 2 fastq files. I tried importing using the Casava 1.8 single-end demultiplexed fastq format but it did not work for my samples as they are not in the correct format I guess?

I am trying to create manifest files for each sample and import them that way, but I can't even get my first sample imported. Yes I followed the tutorial on the Importing Data section of the Qiime2 page and that worked for me, but when I tried inputing my samples into the manifest file from the tutorial and following the exact sample instructions, I get this error message:

/Users/Alex/Downloads/se-33-manifest is not a(n) SingleEndFastqManifestPhred33V2 file:

Filepath on line 1 and column "absolute-filepath" could not be found ($PWD/Users/Alex/Desktop/barcode06-HA/AJN854_pass_barcode06_62ff4951_0.fastq.gz) for sample "Barcode06.1".

Any help at all would be greatly appreciated!

Picture of manifest file:
Screen Shot 2022-09-13 at 1.56.28 PM

I figured this out! All I had to was remove the $PWD and it worked...

2 Likes

@ag1170,
good to hear, on a unix system, when you start with /Users/, it is an absolute filepath, where it does not matter where you are in relation to the file, the computer knows how to find it. This is in contrast to a relative file path, where the path to the file is in reference to where the path was accessed from. This is the sort of path you would need $PWD for, as how to get where your files are is in relation to where you are right now!