fastq.gz file is not in FastqGzFormat: file is uncompressed

[sisalt19]

I searched for this problem and found someone with a similar error... but the forum answers weren't helpful to my situation. I am using qiime2-2022.2 installed with conda on my university's remote access supercomputer that runs on a unix system.

Here's the command's I ran:

unzip -q New-GOPA-Seq-20230207T001729Z-001.zip

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path New-GOPA-Seq \
  --input-format CasavaOneEightSingleLanePerSampleDirFmt \
  --output-path New-project-sequences.qza

[Error message]
There was a problem importing New-GOPA-Seq:
New-GOPA-Seq/220721SB_S240_L001_R2_001.fastq.gz is not a(n) FastqGzFormat file:
File is uncompressed

However, I have run this code multiple times on my other raw sequence files and have never gotten this error. My files look identical to the ones I've run previously, being that all of them have the .gz at the end of them indicating that they are compressed. So I'm not really sure what the issue here is. The line where I unzipped was just me unzipping my raw sequence zip file into a folder of compressed sequences.

[colinbrislawn (Colin J Brislawn)]

Welcome to the forums!

Sometimes, files are named with .fastq.gz even though they are not compressed. (They have the wrong extension, for some reason.)

Try running this and post what you see!

head New-GOPA-Seq/220721SB_S240_L001_R2_001.fastq.gz

If we see normal looking DNA text, we know the file is not compressed even though it has the .fastq.gz extension!

[sisalt19]

I actually just realized that those reads in particular were blank... which would probably explain why there was an issue inputting them. They probably got corrupted when downloading them initially. Apologies for wasting your time with this! And thank you for your help anyway