I am new to QIIME2 and am working through the 'Moving Pictures' tutorial. While attempting to import my data, I received the following error message:
"There was a problem importing emp-single-end-sequences: emp-single-end-sequences/sequences.fastq.gz is not a(n) FastqGzFormat file: File is uncompressed"
Does anyone know how to resolve this problem?
Further details: I'm running QIIME2 through Putty.
When I download that file from the tutorial I get a
sequences.fastq file. I'm guessing what happened is that you downloaded it and then added the
.gz extension manually? The sequencing files need to be compressed.
Are you in some sort of linux environment? You can use the command
gzip to compress your files.
Can you show me a screenshot from your environment of how the command
gzip works in this context? I am indeed in a Linux environment.
I have attached a screenshot of where I am encountering the error.
You can confirm that your files aren't compressed by entering the command
head followed by the path to one of your sequencing files--if you see fastq output and not gibberish then it's not compressed.
Thanks for your help. However, I am struggling to visualise the output. Can you send through a screenshot of the moving pictures tutorial with your amendments? I would love to make sure I am doing this correctly.
What we're discussing is tangential to the moving pictures tutorial. When you downloaded the sequencing files from the tutorial they were probably uncompressed, and now you probably need to compress them. You should use a search engine to read about the
gzip command if you don't understand how to use it. This book is a good resource if linux commands in general are confusing to you.