We started making our input file with BEAUti. The data was consisted of 6 samples. I had previously converted them into NEXUS file, which was the only format accepted by BEAUti. Dr. Miller sent me a paper (estimating divergence time of viruses is close to estimating that of bacteria) and suggested us to compare / discuss our work after working separately for a while.
So, for my part, I entered the date (the day each was sampled) of my samples in months (since Jan, 2001). Then, I moved on to setting the substitution model as was suggested in the paper - HKY. I would like to test out different models later as I have read several other combinations that would fit our data. But for our first run I would just stick with the tutorial.
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| Tips Lane - sampling date |
As for Clock lane, I set strict clock (constant rate) because of the low diversity data we are analyzing. Next is the Tree Prior. The Priors panel allows the user to specify informative priors for all the parameters in the model, which can be helpful or burdensome, especially if no obvious prior distribution for a parameter exists (like in our case). Thus, we would need to try out different settings later. My initial setting shown below.
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| Exponential because bacteria usually grow exponentially |
When all was ready, I clicked generate BEAST file. However, when I uploaded the file to run BEAST, it repeatedly said error! For some reason it said that my setting resulted to 0 prior distribution. One possible reason, in which I read from the BEAST user group online, was that "BEAST starts with a randomly generated tree and if you set tight priors for the parameters, the starting tree may have an extremely low probability which makes it impossible for BEAST to proceed." I went back to the Tree Prior panel and changed random starting tree to UPGMA starting tree. While it ran fine on my computer initially, it terminated to error the next time. After going back and forth, I in total generated 7 files!! Still not working. We decided to make our own starting tree using my mentor's website next time. Yet, the whole process kind of gave me a headache for staring at the screen for 3 hours. To be honest, I am quite intimidated by the computer program as we couldn't really understand the math behind those parameters to fully understand why we were doing. Yet again, those tools are indispensable to many scientists though they would not have invented them themselves. I could only hope that they would start making more sense along the way. Trials and errors - GO SCIENCE!!
Ah, real science! You are in the thick of it now, and you seem to making good progress. Despite the errors, you are making approaches and adjusting your techniques. You will succeed in the end but it may take a few more attempts.
ReplyDeleteI am impressed that you can read, understand and apply primary documents. You seem to be operating at a graduate student level!
Thanks for your great work, as always. Looking forward to the next update!!
Thank you Mr. Calos! The process was indeed tedious, yet I kind of have a sense now how to manipulate my settings to get a good tree. Hope it will become better as we go along:)
DeletePeggy, as one of the managers of the signature program I'll be reading your blog posts this semester. It's sounds like this week was frustrating, but you've got the right attitude. Maybe this next approach will work better for you. In the end, I imagine you learned a lot just from this experience. I look forward to reading more and learning about your project!
ReplyDeleteThanks for the encouragement! I think I am gradually getting what I am doing, and we just made our first attempt to generate a tree!
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