Missing sequence data in FASTQ record

[Brightbeard (Andrew C Eagar)]

Unfortunately, I ran into another snag. Trying to use the quality filtering, deblur, and vsearch commands resulted in an error concerning whitespace in my file. To debug this, I validated my demux.qza file and received the following message:

Artifact demux.qza does not appear to be valid at level=max:

/tmp/qiime2-archive-1mrp3icd/f913f599-1179-4b98-be30-ce6fddc9d83e/data/Sample67_22_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:

Missing sequence for record beginning on line 5157

Clearly, my artifact file isn’t valid. Is there any method to correct this?

[thermokarst]

Hi there @Brightbeard!

It looks like at least one read in Sample67 has no sequence data in it — this is going to cause problems in other methods, beyond those in q2-vsearch. You might need to take a look at your source reads, prior to importing into QIIME 2, and make sure everything is good to go there. You might be able to use cutadapt on its own (or a similar tool) to remove 0-length reads. Keep us posted!