UFBoot does not converge, continue at least 100 more iterations
My job on IQ-TREE has been running for more than an hour.
For my UROP, I’m exploring the role of a bacterial communication system called quorum sensing (QS) in marine microbes, where bacteria produce molecules and behave according to the concentration of those molecules. Right now, I’m trying to build a phylogenetic tree that helps me analyze how similar the protein sequences of certain enzymes that produce QS molecules are.
I text my supervisor.
me: i’ve been running it for A While now and it’s on iteration 700 and every 100 iterations it does that which is very ??? i think i might try to submit it again, but maybe i put it in wrong at the fasta level, not sure tho :(
It’s not an issue with the size of my tree — I’ve only put in about 100 entries, and there are people out there analyzing trees with thousands of sequences.
Turns out it’s because some of the sequences I’ve put in are way too similar, and essentially, the tree search is stuck in a loop, constantly going back and trying to find a better alignment, over and over again.
“I’m so obsessed and fixated on the past,” I tell my therapist today. “I keep trying to process it, but I just keep thinking about it over and over again and it feels so hopeless. I don’t know how to process it any more than I already have.”
“It sounds a bit like you’re just reliving the past, instead of actually processing it.”
I leave the session with the realization that “processing” doesn’t necessarily mean poring over all the details of a past situation and recalling how I felt about it.
Instead, it’s more about making meaning out of things that happen — and that’s the only way to move forward, the only way you break out of the loop.
This summer, I stayed in Cambridge to work on my UROP full time. There are some things that haven’t exactly turned out the way I expected or wanted them to, and this month especially, I’ve found myself curled up in my room, too exhausted and numb to deal with all of my responsibilities.
Still, I’ve done a lot this summer. I’ve made a lot of progress on my research, and I’ll be continuing it as a SuperUROP this year with the Civil and Environmental Engineering department.
It’s been a while since I last blogged. I got plunged into an unyielding pit of writer’s block, along with some personal issues that left me in a general state of “I don’t know what’s going on in my life, let alone how to write about it.” A lot has changed in the past six months. (I’ve missed the blogs!)
To ease back in, I thought I’d make this post a hopeful, positive little update about what’s been going on with me, with lessons I’ve learned along the way.
- Last semester I took five classes, which was a first for me.
- 6.1220/6.046 (Design and Analysis of Algorithms): This is a notoriously difficult class. I dropped it my junior fall right before the first exam because I knew there was no hope for me, the way things had been going. I took it again this spring, and it was still hard, but I passed, and I’m really really proud of that!!!
- 7.05 (General Biochemistry): I think this was one of my favorite classes — it was endlessly entertaining and engaging. There was a lot of material relevant to my UROP as well, as a plus.
- 7.002 (Fundamentals of Experimental Molecular Biology): I needed this class because a lab class for my major wasn’t offered this year, so I took this and I’m taking 7.003 this fall. Chris and I were lab partners, which was fun.
- 21L.487 (Modern Poetry): Back in freshman year, I took 21L.004 with Prof. Tapscott. It was over Zoom, but his unique sense of humor and attitudes toward poetry made it a good time. Being in his class in person this time was a treat.
- 21A.502 (Fun and Games: Cultural Perspectives): Such a fun class (as you can expect from the name!) I’m doing my HASS concentration in Anthropology, and this class brought so much joy to me every week. We went on field trips to Pandemonium Games in Central and Sinha Capoeira in Somerville. It was so immersive and the readings were endlessly interesting — and Prof. Jones is amazing! I’m scheduled to take another class with him next spring :)
- After a couple of rough semesters as I tried to adjust to life at MIT, I achieved an all-A semester this spring! Grades aren’t everything, but this was a really big moment for me.
- In April, I presented a poster at the MIT Microbiome Symposium on my work!
- RIP East Campus, but I’m moving out in two days to a beautiful, airy apartment with friends I adore endlessly. We have color-coded spreadsheets to coordinate group orders? And Tiffany even drew up a floor plan?? I’m excited beyond belief to make this place ours, and to spoil my cat with cute cat trees and unnecessarily fancy litter boxes (it looks like a plant!). Expect an apartment tour at some point.
- I’ve been learning how to knit! I’ve gotten pretty far in terms of my crochet skills, but I’ve always wanted to make socks, which is what I’m knitting right now. Below is a little sample of fiber arts pieces I’ve made in the past few months.
That’s it from me for now. There’s a lot of stuff I’m looking forward to this semester — and hopefully, I’ll get to share those things with you.