Hey there @Cybele_C!
I think you have everything you need right there in that error message!
Path "Manfest1" does not exist.
Based on the screenshot you provided, I agree with that error! I don't see a file called "Manifest" --- but I do see one called "Manifest.csv".
Once you fix that part of your command, you will bump into another problem related to the paths listed in your manifest file:
/Users/cybelecollins/qiime2-skate3/paired-end-sequences/CC1_S1_L001_R1_001.fastq.gz
/Users/cybelecollins/qiime2-skate3/paired-end-sequences/CC1_S1_L001_R2_001.fastq.gz
Those files don't look like they exist to me, either, there are no files sitting in the paired-end-sequence
dir in your screenshot! Perhaps you meant to write:
/Users/cybelecollins/qiime2-skate3/paired-end-sequences/CC1-6/...
I assume there are files in that dir, but I don't know what their names are because the screenshot hasn't expanded that folder.
Okay, the last thing about your manifest that jumped out at me --- you listed the forward reads for pair CC1
as sample-1
and the reverse reads as sample-2
--- this will import as two separate samples, but I suspect what you really want is to import the pair as sample CC1
. Just update the first column to have the sample name for both rows --- whatever name you give it here is the name the sample will have for the rest of the analysis.
Keep us posted!