I have been having a similar problem as well since upgrading to 2019.4. We pooled samples for a few studies with colleagues. I ran our data first, successfully demuxing on the 2019.1 version of Qiime2.
However, once I was done with our data, I upgraded to the 2019.4 version of Qiime2 and have not been able to demux since. I spent time troubleshooting via the forums, such as this post here that suggests the error could have been files being swapped such as barcodes and forward reads. However, I checked this and that is not the case.
Additionally, as a final troubleshooting step, I went back to my data that was previously successfully demuxed on 2019.1, using the same metadata file that was originally used as well as the same emp-paired-end-sequences file that successfully demuxed, and got the same error code below via demux on 2019.4. ![]()
I am trying to reinstall 2019.1 now to see if that solves the issue......![]()
