The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Welcome to the forums at Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at

Database reversion

| posted 23 Feb, 2016 04:21
I have a handful of students who are experiencing database reversion. That is, they have the Linux VM up and running and no problems for a while, sometimes a day or two, sometimes, though, less than a day. Then Phamerator stops working or rather it stops updating or gets stuck trying to update. I check or have them check and the databases server and database have been reset to Steve's server at and the Mycobacteriophages_Draft database. For one student I not only removed the SEA2016 machine but deleted all the associated files. I then decompressed a new virtual machine for the same zip file that was used for my own copy, set up the server and database. Checked that all was working, shut down the machine and sent the student on their way. That lasted a couple days. Then it reverted. Today in class I had three students with the problem so we went through correcting server and database. This evening one of those students emailed that it had reverted to the original configuration.

It is not all students and the only pattern I can see is that all of the ones with a problem are using Macs. But not all Mac users have a problem. So nailing it down to a cause may take some doing unless others have the same problem.

What it seems like to me is that at some point, when they launch phamerator, bzr thinks their copy of phamerator is out of date and pulls in a new copy. Sort of an in silico horizontal gene transfer. When I set up Phamerator on a Linux machine last week the copy that bzr downloaded had the old server/database information. So that seems to be what is sitting on Steve's server. In that case, though my reconfiguring the information has been stable. Why some of the students but not all have a problem is a mystery. At least to me.

Edited 23 Feb, 2016 04:29
| posted 24 Feb, 2016 17:42
Yes the intermittent nature is very curious. Steve has updated the bzr archive with Actino_draft as the default. Please let us know if that seems to fix the problem. If not, then I agree with you, may take some serious doing to track down the issue, so if anyone else is having these issues please post here.
Edited 24 Feb, 2016 17:43
Login to post a reply.