Mikhail Schelkunov

There is an option "-t" that allows you to set the number of threads you want to use.

I'm assembling a highly repetitive eukaryotic genome by Miniasm. The first step of Miniasm is a search of overlaps between reads, performed by Minimap. I suppose that using Winnowmap may...

Miniprot is integrated into Compleasm (previously known as MiniBUSCO) and it demonstrates a better capability of BUSCO genes' prediction than BUSCO itself (which uses MetaEuk) https://www.biorxiv.org/content/10.1101/2023.06.03.543588v1 .

@martin-steinegger The main reason I'm asking is that I'm trying to understand whether Compleasm should be preferred to BUSCO. Their main difference is that Compleasm uses Miniprot while BUSCO uses...

@bakillersky I've found a solution for this problem. After "fast_circ.py denovo" stops with this error, I run "CIRCexplorer2 denovo" separately with a command like this: `CIRCexplorer2 denovo --ref=$path_to_the_file_with_information_on_genes --genome=$path_to_the_reference --bed=./CIRCexplorer2_results/back_spliced_junction.bed...

For those who also experience this problem: I've made a workaround. I've created a copy of the BUSCO depository at http://mikeshelk.site/Data/Folder_compatible_with_Compleasm/data/ . If the original BUSCO depository isn't accessible in...

I have the same problem with Dorado 0.7.3. However, Dorado 0.7.2 worked without this problem on exactly the same input file. Either VRAM requirements of Dorado increased, or a bug...

@simonhayns Thank you. "--infer-threads 1 -b 64" and "--infer-threads 1 -b 32" still required too much VRAM, but "--infer-threads 1 -b 16" worked for me.