The problem it's complaining about is that it's trying to dump logs from Docker, and it can't because we never fixed it to decode the logs from bytes, which we need to do now in Python 3:

But the underlying problem is that vg's Docker doesn't seem to be running for it:

courtyard 2020-03-03 11:09:29,288 MainThread WARNING toil.leader: kind-run_gcsa_prune/instancevaqvqh2v    Message: b'/bin/bash: line 1:     8 Illegal instruction     (core dumped) vg prune small.vg --threads 1 --restore-paths'

It looks like the Docker container image that toil-vg wants to use by default is built with instructions that Courtyard can't execute, because Courtyard's CPU is too old. You can reproduce this:

docker run -ti --rm quay.io/vgteam/vg:v1.21.0-132-g46fe0722f-t353-run /bin/bash
wget https://github.com/vgteam/vg/raw/master/test/graphs/snp1kg-brca2-unsorted.vg
vg prune --threads 1 --restore-paths snp1kg-brca2-unsorted.vg >/dev/null

If you use quay.io/vgteam/vg:v1.22.0 instead, the latest released vg version, it works; I think we changed our build process since that old container image was built in order to avoid this problem.

So the fix is:

1. Change the default VG image in toil-vg (and make sure it didn't change anything that toil-vg relies on)
2. Fix the error logging to work right in Python 3

Thanks for this, Adam. Looks like this fixed it, though it got hung on test 13. I unfortunately did not keyboard interrupt the test, so I didn't get the test report to see what happened. I am running the tests again though.