Error importing fastq files using “Fastq manifest” formats

[thermokarst]

Ah ha!

@EGA

I used the -cutadapt command maybe it is causing the problem?

Yep!

Check out this post for a workaround!

Cutadapt thinks my fastq.gz files aren't fastq.gz

Woohoo!!! !!! With that little bit of data you provided, I was able to reproduce the error. Not only that, but I was able to see () exactly what the issue is. Running the same command you provided above, but instead of using q2-cutadapt we go through cutadapt directly, I get some reads out of cutadapt that look like this: [00%20PM] Yowzah! So, hopefully that QIIME 2 error makes a bit more sense now --- it was complaining about records that had no sequence as…

Let us know if you need help with any of that!