Plug in error from cutadapt

[ebolyen (Evan Bolyen)]

Hey @JoseM,

Thanks for the log! Your environment looks like it's 2018.8, but in your log, the software says its from 2018.6:

/home/jmseoane/miniconda2/envs/qiime2-2018.6/lib/python3.5/site-packages/...

What does qiime info say?

Noteably, there was an issue with trim-paired in 2018.6 and we released a patch version for it (2018.6.1):

Incorrect results produced by q2-cutadapt's trim-paired

Summary We recently discovered a bug related to the q2-cutadapt plugin’s trim-paired command that, in certain situations, can produce incorrect results. In particular, the forward and reverse reads are swapped, causing the underlying cutadapt command to apply the forward read trimming parameters on the reverse reads (and vice versa). Impact This issue impacts the following versions of q2-cutadapt: 2017.12 2018.2 2018.4 If you think you may have been impacted please check your provenance at h…

It's possible you've run into this inadvertently. The reads listed in particular seem to be the wrong direction for the file they state they are coming from.

If your 2018.8 environment is accidentally using 2018.6 it's possible that's the reason for the error.