Power outage kills 34 million state BEAST run, Investigator contemplates Linux homicide

As the title suggests I walked into the office this morning to two computers…both shut off. Now no one touches my desk especially when I have analysis running and we had a huge storm last night with lightening and wind and although Bangkok is a ‘1st’ world entity of itself some days the fact of the matter is, I live in a 3rd world country that is 98% agriculture. The result? 34,510,000 iterations of a BEAST run of 100 million completed and the analysis ends with the power cutting off. My poor linux, diligently plowing away at iteration after iteration, only to be thwarted when its attachment to life power is cut.

CURSES!

A check in tracer reveals that my posterior, prior, likelihood, tree likelihood and coalescent are all at ESS values in the red (under 100) and clock.rate is under 200 (in the yellow). So things have not finished ‘mixing’ and converging altogether.

DOUBLE CURSES!

Thankfully I started the same run on the Oslo Bioportal August 23, 2011 and currently the status is on resource/started. Unfortunately they do not give me an up to the moment snapshot of my analysis and I cannot check using Tracer with it along the way so it will march to 100 million generations until it is done. I was hoping to track my run as it went to see if it exhibited good mixing and convergence prior to 100 million iterations– but alas, I will never know. And if Oslo has a power outage–then the ‘gnomes’ or ‘gremlins’ are up to something … little bastards.

There’s something comforting about watching status lines flip by on an analysis, lets you know the computer is hammering away at the brick wall of analysis trying to find that one loose brick. That’s why I always like to run things on the terminal although I have to say the GUI for the program is quite pretty. Yes, I just called the GUI for a Bayesian analysis program ‘pretty’– sometimes I indulge in superficial scientific vanity.

So I’m torn on whether to restart the analysis from iteration 0 or wait for Oslo to cough up my results. Without status lines to watch much of my previous list of things to do while BEAST runs gets nullified… I guess the ‘analyst’ will have to actually go outside… see the sun… get some fresh ‘non-circulated’ air… engage in social behavior with others perhaps also affected, having lost analysis down the black hole of power outages and now venturing forth confused from their cave like offices into the bright heat of Bangkok… or I need to find a new program with status lines that takes a long time to run!

~cheers.

Things to do while BEAST runs

So in the world of molecular evolution one of the cu-de-gras-de-analysis programs would have to be BEAST. A power-packed bayesian analysis software that makes phylogenetic trees, calculates the time to the most recent common ancestor (tMRCA) and substitution rates, geographic partitioning, can handle copious amounts of data and pretty much squeezes blood from a turnip…walks on water…heals your mother, in short, it’s cool.

Sound awesome? It is. For a more technical in depth discussion and introduction to BEAST software I suggest reading the Wiki and attacking the tutorials with full force as well as reading some awesome books on phylogenetic inference such as The Phylogenetic Handbook. If you are super impatient and channeling your inner terrible twos about phylogenetic analysis then read Phylogenetic Trees Made Easy. It has a nice introduction and literal button for button how tos on different software packages including Bayesian ones. When you’ve finished your tantrum, enter the adult world and read Felsenstein or the phylogenetic handbook mentioned above. Now that you’ve been introduced to phylogenetic inference and genetic analysis with forays into evolution over time…jump into BEAST. Although the BEAST wiki and manual are still navigate-able without that background but you’ll be scratching your head a bit and heading to google for answers.

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