q2_cutadapt tests fail with FileNotFoundError under Debian

When I run the q2_cutadapt tests under Debian with qiime 2019.10, most reliably fail with FileNotFoundError in /usr/lib/python3.8/shutil.py. This is tracked as debian bug #956220. In an answer here, it was hinted that other people have similar issues. Is there a known workaround?


Hi @adrianheine, thanks for the post.

Just as a quick note, at present QIIME 2 is only “officially” compatible with python 3.6 - we do not support 3.7+ (yet), although we are hoping to work on this a bit later this year.

So, taking a closer look at the build log you linked to, I think the error isn’t specific to q2-cutadapt, but rather it points to a small issue in the QIIME 2 framework:

There are a few invocations of shutil.copytree in the provenance module:

One of the things that @ebolyen built out to address these cross-device linking errors is this util:

We should probably do a sweep of the framework and make sure we are using that util where needed.

Thanks @adrianheine! I’ll bump this up in priority for our current dev cycle - the next release of QIIME 2 is slated for late May 2020.