Unfortunately, most of this month’s goals are the same as last months!
- Process Olympia oyster GBS data. I’ve been running two different analyses (Stacks and PyRad) on two different machines (Hummingbird and Roadrunner, respectively) and I keep encountering different problems! For example, just yesterday, the following popped up in Terminal on my SSH connection to a Docker container on Roadrunner running PyRad in a Jupyter Notebook (click on the image to enlarge):
(http://eagle.fish.washington.edu/Arabidopsis/2016-06-30_screenshot.png)
The computer became completely unresponsive (for the second time in less than 24hrs). Maybe the problem is Docker. Maybe it’s creating a remote tunnel to a Docker container. Maybe it’s running Jupyter Notebook through a remote tunnel into a Docker container? I don’t know. At this point, I’ll just install PyRad directly on Roadrunner and try to get the analysis done that way. It certainly isn’t convenient because it means I have to be physically present at Roadrunner to execute commands and check on things…
Get stuff running on Amazon AWS and Hyak as soon as possible. I think the increased computing power will improve my chances to actually complete the Oly GBS analysis due to the greater stability those computing environments provide.
Quantify coral DNA methylation. This should be straightforward and completed on Tuesday, 20160705.