Importing fastq.gz files

Hello, I am new to qiime2 and I have gone through most of the tutorials already with success. Now I am working on importing my own data using the cassava 1.8 paired-end demultiplexed fastq tutorial. I keep getting an error message that the file cannot be found or opened. The file contains unzipped fastq.gz forward and reverse files in the format of “CS422-frag-17_S17_L001_R1_001.fastq.gz”. I do not understand why these cannot be opened and have tried multiple methods of renaming the files as well as the major file containing the data. I have also looked at the manifest format but I do not understand how it would be able to access my files if it cannot already. Thank you.

Hello @smith13mr!


We will need a bit more information in order to help you:

  • What version of QIIME 2 are you running?
  • What was the exact command or commands you ran? Copy and paste please (or screenshot).
  • What is the exact error you are seeing? Copy and paste please.

Also, it would be helpful for a screenshot of your data directory.

Hmm, the gz extension actually stands for “gzipped,” a type of zipping protocol - are you sure these files are unzipped? If so, their extension should probably just be .fastq (but, first things first, let’s look into results from my questions above).

Anyway, looking forward to hearing back from you! :t_rex:

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