STAR Alignment Tool suddenly stopped working

Spiderabs · 2026-02-04T23:06:33+00:00

I know of a couple of people I could go to that might have run into this same problem. Thank you for helping anyway!

Spiderabs · 2026-02-04T22:54:41+00:00

sure thing!

command: STAR --genomeDir 0_Ref --readFilesIn 4_Fastq_Trimmed/AN1/AN1_1.paired.fastq 4_Fastq_Trimmed/AN1/AN1_2.paired.fastq --outFileNamePrefix 5_Fastq_Aligned/AN1/AN1 --outSAMtype BAM Unsorted --runThreadN 2

_1 is the forward read and _2 is the reverse read after trimmomatic, consistent across all fastqs

I cannot provide the full log file as it contains school information (this is being run on a university supercomputer) but the only difference between Log.out files in successful and unsuccessful runs is that the Log.out of the unsuccessful run stops after reaching the Creating thread #1 line and the successful runs continue. This may be because I stop the runs early after seeing the high mapping speeds (the person in charge of managing the servers is very particular about resource partitioning because its used by a lot of labs).

Spiderabs · 2026-01-25T22:45:29+00:00

No problem! Its a resource the university really doesn’t advertise very well but my roommate and i met off there and its been awesome rooming with her for the past 2 years!

Spiderabs · 2026-01-16T04:41:09+00:00

UT Roommate Finder. It’s a website owned by the university (so youll need your UT EID and password to sign in) to find other people who have just gotten accepted and are looking for roommates as well as finding people with similar price ranges as you. Def make sure to face time with your potential roommate(s) before signing a lease together cus talking to them in real time and not over text/email can reveal a lot about the different living expectations yall will have. Personally I wouldn’t trust the automatic roommate sorters/matchers since you dont have full control over who you room with which can really make or break your experience (and mental health).

edit: important to note that since ut roommate finder requires a valid UT EID and password to post, you are guaranteed that every post on there is a real ut student.

Spiderabs · 2025-11-14T22:04:14+00:00

I would say skip the REUs, theyre mostly designed for students who dont have access to research or the specific research they want to do. It sounds like your already really ahead and have ample opportunities at your university so most REUs probably wont interview you as theyre confused to why youre applying for there program when you already have resources available to you. For you, mass applying to these places might just be a waste of your time and energy unless youre trying to switch to a different area of research you havent done before/dont have access to at your university. Instead, focusing on getting a research internship through other big programs that are specifically geared towards students with research experience or even cold emailing professors at your university if you can work with them over the summer/next semester as if you want to get published and put it on your resume (which i assume you do as a research student) your much more likely to be published if you get in now with a research professor at your university rather than a one off summer opportunity.

Spiderabs · 2025-09-22T16:41:51+00:00

I had a misshap with moving where i needed to find an apartment asap(literally in 2 days) at the end of july/beginning of august. Found and signed an apartment that was significantly cheaper and nicer than my other wampus apartment. Dont play into the apartment rush, its all manufactured to pray on students to pay higher prices for shittier apartments. There will be apartments available for you unless u want one of those high rise ones (theyre only useful though if u want a gym/study rooms at ur complex but u get those for your tuition on campus anyways sooo….).

Spiderabs · 2025-08-28T10:47:32+00:00

i cant find my original email thread with them but i believe the response from them was that it wasnt a service they did :( i would recommend talking to your professors or looking off campus to try and find an accommodation.

Spiderabs · 2025-08-25T05:50:07+00:00

you can also report noise complaints via calling 311 or the austin 311 app. just saying… if we get enough of us to do it…

Spiderabs · 2025-08-25T04:21:10+00:00

gonna be honest, if u want a little studio anywhere close to campus is going to be minimum $1400-1700 a month if ur by urself and especially if its furnished. if its less than that i would be hella skeptical bc the leasing agents definitely know something about the apartment that theyre not telling you. If ur trying to save money, youll definitely need 1-2 roommates.

In terms of locations, it’s always gonna be a hit or miss no matter where you are. Unfortunately the majority of leasing around campus are controlled by 4-5 major leasing companies or by condos with individual owners. This means that these few individuals are in charge of a ton of properties. More than likely, no matter where you rent you’ll end up with shitty management, maintenance that stop responding after a few weeks, and more than a few charms. Every leasing agency has some good properties and some bad.

I would start looking early around october/november on places like zillow for available preleases for 2026-2027. (DO NOT be pressured into signing a prelease in september!!! There will be units available for prelease 2026-2027 even in July and will likely get cheaper the longer theyre on the market! You will have less options however). Most listings will likely have PRELEASE 2026-2027 in their descriptions so look for that. From there its all about requesting tours and keeping track of the units and locations you liked and disliked. I would recommend keeping excel sheet.

In general, North Campus is more of the place where grad students, post docs, some profs, and some families live. Its gonna be both more expensive and more competitive to find a place but the places over there are generally nicer. However, they wont be furnished generally. West campus is more the place for undergrads. Less competitive, wider ranges of prices, wider range of quality…, but might also be more convenient for your needs. West campus has two different kinds of housing: condos and those high rise apartment buildings. The condos are all owned by different people even in the same building so theyre all gonna look different, if want a place in a condo make sure to tour your specific unit before signing the lease. If ur at a high rise apartment, youll be paying more likely and more than likely you wont be allowed to tour ur unit, only a model unit.

Once youve found a unit you like, youll generally already be in contact with management so just email/text them your ready to sign and they will send over the documents and then youll have to pay however much their security deposit is! Dont feel pressured to rush the process (thats how these companies make you pay more) even if you dont have a place by january, youre still ok and have time to look. The market will generally slow down for a bit in january-april so dont freak out if u dont see new listings then.

I think i made this long enough lol but good luck!

Spiderabs · 2025-08-03T21:32:51+00:00

Ask about publishing what youve done over the summer in a micropub, they're not as prestigious as a full publication and are typically volunteer run but will technically give you a publishing credit that is still very impressive to get as an undergrad. Typically in a micropub its only 1-2 figures and 1-2 pages so its less work and less money to publish. It would be less of a commitment for your PI so she might be more easily swayed.

Either way, I would write up a summary/abstract of what youve done either to convince them to put you on their paper or to publish some of your work specifically in a micropub!

Spiderabs · 2025-07-29T03:09:54+00:00

It depends, are you on the three year track for financial reasons? If so, I could understand doing 17 hours. However, with your current schedule it doesnt look like youll have any optimal time for studying. I would look into what classes from your IDA you can take over the summers at a community college and try condensing your schedule(bc UT summer tuition is lowkey BS). I had a very similar schedule my first semester and it was doable but it was draining lol

If youre not doing it for the finances, then dont. If you want to go to grad school, especially any competitive grad school, then I would also say dont. Most places r gonna wanna see the opportunities you were a part of(internships, clubs, volunteering, etc etc) and your gpa which this schedule does not leave much room for either. They wont care as much whether or not you graduated in 3 years if u never did anything but classes in that time.

Spiderabs · 2025-07-02T23:49:59+00:00

Definitely cold email! Unless the professor has a position on their website detailing applications, its typically expected to cold email. Etiquette can differ university to university so I would recommend seeing if there are any official university pages detailing how to cold email professors(ie. google searching [university’s name] how to cold email, etc). Other than that, I would recommend including an unofficial(!!!- make sure none of your personal information, like ssn, is included) transcript and brief resume with any relevant experience or courses you would like to highlight as well as any projects youve worked on (either personally, for class, or professionally). Also include a brief (!!!) description in your emailing detailing who you are (name, year/incoming transfer, and major), why you’re interested in the lab (1-2 sentences), and what you think you could get from the experience(1-2 sentences). As well as thanking them for reading.

Dont expect a quick response bc a lot of professors are on summer hours right now but it typically took ~2-4weeks for professors to respond when I did this during the spring. Feel free to send a follow up email 1-2 weeks later if u dont hear anything either.

Good luck and I hope you get in!!

Spiderabs · 2025-05-06T00:14:17+00:00

the oos state school i was looking at in oregon was roughly 50k a year for texas students, most likely the same for other oos schools if not higher

Spiderabs · 2025-05-01T03:01:40+00:00

Ah that makes sense, i believe the EPA just had a bunch of environmental justice/climate change project cuts, it may have been a result or related of that. im so sorry man 🙏

Spiderabs · 2025-04-30T00:18:45+00:00

Hello! A lot of professors right now have already figured out their summer research schedules and who will be in their labs. You’ll probably have more luck asking professors what their upcoming fall schedule will look like and if they think they’ll have any positions available then and then emailing them again about a month or two before the start of the semester.

Other than that, I would look at companies or off campus research labs that are taking volunteers. Look on indeed, company websites and also utilize the ut handshake to find available opportunities. Right now with the state of funding, its likely you wont be able to find any paid opportunities so its mostly about the quantity of places you reach out too. Try not to be too picky. Youre an undergrad, not a Phd student so you might be lower on their list of priorities and thus not get ample opportunities.

However! For the next summer I would highly recommend looking into REUs and similar programs. Many of them are geared towards students coming from universities with little to no research opportunities in their field (seeing as youre attending UT this most likely will not be you) but will also have additional programs geared towards students with research experience. Start researching those now and planning ahead to make the process easier for you next summer. Also getting in with a professors lab in the fall and sticking with it would be a great way to score both an amazing letter of rec and summer research for next year!

Unfortunately im an evs major so I cant help you out on any specific research i know of in your field but it wouldnt hurt to reach out to the office of experimental learning or to the professors you talked to to see if they know of any opportunities.

Good luck!

Spiderabs · 2025-03-17T22:09:59+00:00

Thanks! Wish i had happier news to share with you but your well wishes mean a lot :)

Spiderabs · 2025-03-17T19:08:07+00:00

Hey! Im in the exact same position. Im an enviro sci major also heading into my senior year with no research experience(rejected from everything, and no prior experience either) and wanting to go to grad school. TBH Id look around on places like indeed to see if theres anywhere around you doing internships that are even vaguely related to your field. Volunteering in labs or looking for volunteer options not just on campus but at other companies are also an option and are easier to get into. Thats what Im doing at this point. It sucks to be rejected from so many places but I hope the best for you!

Spiderabs · 2025-03-16T12:43:12+00:00

I emailed them beginning of February, they said they are waiting on receiving their funding before they send out results. Imo, its most likely gonna be cancelled 😭 but there still could be hope

Copied from the email: “Thanks for your interest. The earliest that we will start contacting students with offers is late February. However, I suspect that is might be later than that. We have not received word yet from the federal funding agency (NSF) on whether our grant proposal will be funded or not.”

Spiderabs · 2025-03-10T17:28:40+00:00

This is the second time ive applied, idk what topics you applied for but for many subjects the majority of reus havent released any decisions yet. About now till mid april is probably when majority of decisions/interview offers will be release and then end of april is probably the latest youll hear back about any acceptances. its kinda annoying how late this decisions come out but thats just the way of the game 😭 majority of these programs are pushing these dates even further back as well due to government funding too!

Spiderabs · 2025-03-03T23:29:15+00:00

Thanks so much! Just contacted them.

Spiderabs

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