I am attempting to import some data into QIIME2 after the new update (2023.5) via conda! My paired-end samples should be imported using the Casava 1.8 paired-end demultiplexed fastq (two files for every sample). However, when I run it, I get the following error message.
Hello @zahra. This error means there is no file called "casava-18-paired-end-demultiplexed" in the directory you are trying to run the command in. Make sure you are running the command in the correct directory and make sure you spelled the name of the file correctly. Thank you.
Hello @Oddant1 ! I'm so sorry as I'm relatively still new to QIIME2. When you say directory, do you mean current directory I am working in? QIIME2 itself is in my parent directory, and when I work off of the importing tutorial in the same location as my data (a folder in desktop), the code works for the tutorial but not my own data.
It looks like you are doing the tutorial in the ~/Desktop/01_data directory and your own data is in the ~/Desktop/2022_Data/01_data directory.
The --input-path argument takes a path to a file on your computer. A file with the name casava-18-paired-end-demultiplexed exists in your tutorial directory because it is part of the tutorial data you downloaded. The name casava-18-paired-end-demultiplexed is not set in stone, you need to replace this with the path to the data you are trying to import.
It looks like a file with the name casava-18-paired-end-demultiplexed does not exist in your own data. You most likely have a file with a different name in your data that you need to import. If you run the command ls while in the directory that contains your own data, it will show the names of all of the files in that directory. You will need to use one of them in place of casava-18-paired-end-demultiplexed when importing your own data.
Ah, I see now. I completely missed that the casava-18-paired-end-demultiplexed is referring to the directory/folder containing the sequences and had assumed it was the program that was missing itself. Thank you so much!