Minimap2 vs Last running time about nanosim

[cheny19]

Hi Natasha,

When NanoSim enters model fitting phase, it has nothing to do with the aligner any more. read_analysis.py was trying to find the best parameter combinations for the error model and it took nearly 10 hours for the alignment results from minimap2. Could you send me your alignment files or raw data so I can test? I'm curious why it took so long.

Thanks,
Chen

[npavlovikj]

Thanks for your reply and explanation @cheny19 .

I used two different datasets, and in both cases the run time with "minimap2" was significantly longer.
Please find the datasets uploaded here, https://drive.google.com/drive/folders/1p9OSIXseyGoXoKv9oNYaoP8PhaLqYygI?usp=sharing.
I used "nanosim-2.0.0", "minimap2, v2.10-r761" with 4 threads, and "last, v876".

Please let me know if you need any additional information.

Thank you,
Natasha

[cheny19]

Hi Natasha,

Sorry I didn't reply until now. Last few weeks I looked into the code and I think the runtime is heavily dragged down by R. So I re-wrote the model fitting part in Python (which is faster than R) and it now supports multiprocessing. The model fitting stage can be finished within a hour now. Please download the latest commit and have a try. I haven't made the new release yet, because I have more testing to do, but on your dataset, it works fine.

The error model is a bit different between minimap2 and LAST, and the original proposed model may not fit very well on errors inferred from minimap2. That is also why it ran for so long in previous versions. NanoSim will throw a warning if the fitted model cannot pass statistical test, but don't worry, it's still close to the emprical errors. I'll keep looking and see if there are better models.

Thanks for pointing this out!

[npavlovikj]

Hi @cheny19 - all this sounds great - thank you so much for improving NanoSim!
I will have some time next week to test this out if that is ok.
In the meantime, does this mean that I can still use the simulated reads generated by Minimap2 in the previous version, or I need to re-run the simulation now?

Thank you,
Natasha

[cheny19]

You can still use them.