Hi,
Thanks for the extra info, but it's still not really a reprex as I can't run this code or have an idea of the input files. I understand this is very difficult to provide as fastq files can be huge. Judging from the output you get, here are some questions / remarks:
- Did you use the tutorial data to test the whole pipeline and see if it runs error free? Often when there is issues with packages, paths, etc you'll encounter them there first, and it's way easier to debug
- When you list your files, I don't see a .fastq extension. What are these files? (e.g. Sample_TA-2423-Rhizo2Ser205-1-EKTO)
- This line:
fnFs <- sort(list.files(path, pattern="_R1_001.fastq", full.names = TRUE))seems to be a copy paste from the tutorial, but I don't see any files you have that end with "_R1_001.fastq" (what it does is it selects all fastq file names from the folder and extracts the name). This is where I think things go wrong, because in your case this will be empty and nothing will happen down the line and generating errors likereplacement has 1 row, data has 0
I suggest you try the tutorial and your code side by side and see where yours starts to fail. I think fixing the files names will already get you to the next step.
Good luck!
PJ