Joel Armstrong

Can you dump `/var/lib/mesos/mesos-master.INFO` from the master? it's probably long as fuck, but I think you can attach it.

Oh, yeah, I forgot to ask. Are the jobs marked as preemptable? I think by default jobs are considered non-preemptable. From looking at the logs it looks like the nodes...

Hi, Sorry for the delayed reply. Sorry to hear that things aren't working correctly too. It's interesting that this isn't progressing at all and the python processes seem totally stalled....

Hmm, it sounds like the database crashed, or at least became inaccessible. That could be for any number of reasons, but if it's not just some random fluke, it's likely...

Oops, sorry about that. I was thinking of the newer toil syntax. progressiveCactus *should* restart just fine without the `--restart` option.

Hmm, weird. The N50 of the assemblies shouldn't really have much of an effect on the memory usage. Are all the assemblies soft masked? Unmasked assemblies can cause really high...

Yes, that sounds great. Thanks for helping to track this down!

This is a "feature" of the [jobTree](https://github.com/benedictpaten/jobTree) framework. It tries to resume a run if the jobTree already exists, but you're right, it doesn't properly delete it on completion, which...

Hmm, that's interesting. The runtime of running (A, B) then adding C should be about the same as the runtime for running ((A,B),C). Internally we do that exact type of...

Yes, exactly. The reconstructed ancestor needs to be extracted from the hal file into a fasta file. You can run `hal2fasta first.hal Anc1 > anc1.fa`, assuming the first alignment is...