You mention you have 2 files - barcode3 and barcode6. From what I can tell, each of those files are in a folder you’ve called
When I’ve imported my data (Nanopore derived or otherwise), I’ve used the manifest format approach you’ve linked above, and like what you’ve attempted to do in the second of two screen shots.
I noticed you’re passing the name of the directory (
fastq_files) for the input argument, and I suspect that’s where your error is coming from.
Here’s the silly/confusing thing: when you try to follow their directions in the import tutorial using an EMP-format what you are supposed to use as the
--input-path parameter is the folder name (which is what you did in your first screenshot). However, when you follow their tutorial for manifest style imports, the same
--input-path parameter is not the folder name, rather, it’s the manifest file itself.
Assuming you’ve created a manifest file following their guidelines, you just need to switch up one value in your second screenshot: substitute
fastq_files for whatever the name is for your manifest file (if it’s not in the same directory as where you are executing the command, make sure it’s the full path or use an environmental variable set to that path).
That should (hopefully) do the trick.
One follow up question for you and one other comment:
Question: did you filter these reads already? You absolutely should have already corrected these reads with Nanopolish prior to trying to make some sort of taxonomic classification… these reads are far noisier than standard Illumina ones that the denoising algorithms defaults are used to… though note that DADA2 is now making headway into correcting long reads (though these are PacBio data thus far), and I’m not sure if QIIME’s current DADA2 plugin can do anything reasonable with Nanopore reads. That’s on my fall 2019 to do list, so I can’t help you there yet. Maybe @benjjneb can speak to what DADA2 can do in QIIME with long, noisy reads.
Comment: You don’t need QIIME to do any of this. I love QIIME and continue to find more ways to use it’s tools in my projects, but you may want to look at other tools like Centrifuge to get started with packages built for Nanopore data primarily (when it comes to taxonomic assignment).