Hi,
Since this question is a downstream issues from a questions posted elsewhere on this forum, we might wait answering this until the previous one has been resolved (which might fix this one too)
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 …
PJ