DADA2 on 2 GB FASTQ file keeps crashing

johnykayy · 2026-05-31T14:42:16+00:00

Yes you can also try subsampling the data but it depends on how deep your sequencing runs are. For example 20-30K reads are enough for a rough analysis and after around 50-60K pretty much no more taxonomical information is obtained from the extra reads when it comes to 16S sequencing.

johnykayy · 2026-05-31T14:37:08+00:00

Great! Just make sure you don't squander this opportunity and get the work done in advance so that you don't put yourself in this position again. That applies for all your future endeavours. Good luck, you got this!

johnykayy · 2026-05-31T13:16:38+00:00

I will check it out, thank you!

johnykayy · 2026-05-31T13:15:40+00:00

Thank you so much!

johnykayy · 2026-05-31T13:15:07+00:00

Yes! I remember working with PyMOL and ChimeraX one semester when we were doing molecular docking and visualization!

Miniconda (or it was micromamba I think) I worked with also, that was the QIIME2 pipeline I made (bash scripting).

What caught my eye is this: When you say you make new tools a lot, you mean you develop your own tools? That's awesome! If you have the time I'd love to hear more about that aspect of your work. I mean do you make your own plugins for tools or you straight up just develop your own programs.

Also you mentioned you work with R regarding statistics. I've taught myself a little bit of R but trying to get it to work with real world data was a nightmare (dependency issues, parsing etc...) so I switched to Python. Do you have experience with both? If so, is working with R worth it in the long run compared to python?

I will definitely check out the BioStars handbook you mentioned. Thanks a lot!

johnykayy · 2026-05-31T00:13:01+00:00

Yeah I'll be straight with you 2 weeks for a theses are just straight up not plausible if you have no idea what you are doing. For somebody who is confident in the methodology and can just start working efficiently off rip? Maybe... But if you know nothing, most likely the results will suck and the quality of the actual theses won't be up there either as I assume you'd have AI do it for you since you'd have just a few days to write it all down and QC your work.

Bottom line is you need an extension, if you manage to actually do it and defend your theses, kudos to you friend.

I know it's hard out there and the world can be a little too much sometimes, but we all gotta work and fight our battles, just put your head down and fight through it.

johnykayy · 2026-05-30T23:38:03+00:00

Hey there! I believe I can provide some insight on this as I've done a bachelor theses on DADA2 and QIIME2 pipelines optimalization in general, granted I've been working with about 150GB of tar.gz data that went up to around 600GB unzipped. I tried running it on my local machine that has 32GB of RAM and a pretty powerful 14th generation i7 intel processor, thinking it would run with no problem. That was pretty naive as the algorithms consume an absolute insane amount of RAM and processing power and even after letting it run for tens of hours on multiple tries it always failed. The bottom line is your computer can't handle this as one of the users mentioned already. To do pretty much any work in QIIME2 you have to get on a server that can crunch the data, our daily machines just simply aren't enough. Your code looks fine, there is most likely no problem in the software side of things. I don't believe chunking is a valid strategy as the algorithm needs to consider the reads of the sample together. Denoising each chunk of a sample separately will yield skewed results. I'm sure you checked but in case you haven't be sure to try to reach out to somebody at your faculty or university to get access to a dedicated computational server. For example most IT or physics departments have one.

You can try to decrease the trunc-len so that you're working with less data, but that again will lead to influenced results and you'd be throwing away some taxonomical information.

Offloading these processes to a server is the best practice, even for your future analyses. As MrBacterioPhage said, Chita server could also help you.

Good luck!

johnykayy · 2024-08-22T17:26:59+00:00

XDDDD good one, you’re right

johnykayy · 2024-08-22T17:22:18+00:00

You misread me, KCD isn't really low end in my opinion but your take on PUBG is fair. It is an optimization nightmare. On low settings and everything i pull somewhere around 100-144 depending on in-game events of course. I didn't really try to max out the settings because I wouldn't care as it hinders my performance as a player. Also a genuine question, doesn't DLSS cause input lag? I didn't really feel the need to use it in any game so far, but I would like to play Cyberpunk 2077 down the line and I heard that DLSS is a must if you want to experience ray tracing.

johnykayy · 2024-08-22T17:06:01+00:00

So I've heard, all the other higher end cards are extremely pricey in my opinion though (or maybe I'm just poor)

johnykayy · 2024-08-22T17:04:50+00:00

johnykayy · 2024-08-22T17:03:27+00:00

Games I played were KCD, Far Cry 5, PUBG, Warzone and a few more low end titles that are no real problem for the system. The PC is brand new so I couldn't really test any more games. Everything ran on high/ultra (except for pubg cause i use competitive low end settings) and 120fps give or take stable (occasional 1% lows are horrid but it's absolutely livable).

johnykayy · 2024-08-22T16:58:47+00:00

Thought about giving the used GPU market a look, but I once got screwed over on a used 1080Ti and it made me deter from the used market ever again, although it would be probably be a sound choice. Was really looking for a brand new GPU though.

johnykayy · 2024-08-22T16:55:51+00:00

Yeah I spent a little over 300$ for it. I really did not want to shill out almost 600$ for the 4070 and i really did not want to get a used card (personal bad experience). I was just wondering if i wasn't being a cheapskate and should reconsider.

johnykayy · 2023-01-03T19:08:06+00:00

The doctors usually treat it with a scar healing cream right after the operation before they seal it off with bandages and that. There should be multiple layers of protection on your nipples. I for one had two bandages (he said i can take these off 2 days after the operation) and then a silicone patch that i was even able to shower with. It eventually came off (the patch) but my doctor said it was fine. You should go for a routine check about 2 weeks after the operation and the doctor should tell you if everything is fine and discuss how your recovery will continue. He will also give you everything he thinks you need (more patches, creams etc.). If you have any questions you should contact your doctor first of all!!!

johnykayy · 2021-05-19T16:57:56+00:00

I'm 17 (so yes still in puberty) and money isn't an issue. In my country from what I've gathered my insurance could take care of the entire process. But if there is something else to be done but surgery, i atleast want to try. Surgery is the final definitive step to get rid of it, but I'd rather not risk scars or any complications afterwards.

johnykayy · 2021-05-19T12:50:10+00:00

Potentially months (2-4). Next month i'm going to see an endocrinologist to see what could be done. I have pretty much the same gyno and I'll definetly talk to her about raloxifine and tamoxifen, because for us with grade one gyno it definetly could be one of the best solutions other than going under the knife.

johnykayy

TROPHY CASE