SemiBin

SemiBin copied to clipboard

SemiBin doesnt complete bining. Seems to be stuck

3

Hello, So I have been trying to run SemiBin2 on an assembled set of contigs. however, it seems that after generating the training model there is no progress made. I...

HitMonk

Extract then merge

5

When processing large-scale samples using `SemiBin multi` binning mode, `data_cov.csv` and `data_split_cov.csv` may require 1TB+ memory. This PR is dedicated to extracting sample-wise contigs coverage first and then merging, which...

alienzj

Error when running SemiBin2 (normalization?)

6

Hello, I'm running SemiBin2 to my dataset with the multi_easy_bin option. Everything seemed to work properly until it failed with something related to normalization. Any idea of the issue cause...

eperezv

KeyError: '40075' Easy coassembly binning mode

2

Hi, I reported the following error. 2024-02-07 10:09:00 rasputin SemiBin[3664292] INFO Training model and clustering. 2024-02-07 10:09:01 rasputin SemiBin[3664292] INFO Start training from one sample. 2024-02-07 10:09:13 rasputin SemiBin[3664292] INFO...

gabrieleghiotto

Hello, When I use semibin2 for multi-sample binning to generate the sequence features, semibin2 outputs a sample-wise fasta file with contig names provided after the separator. It might be better...

adityabandla

Hi, I'm trying to update the Galaxy wrapper to SemiBin2. With SemiBin2 there is the problem that 4/6 test cases have an empty output, while with SemiBin1 there was an...

Ralwoss

Semibin not respecting `-p` threads argument

1

Thanks for the fantastic binner! I'm getting many more bins from Semibin than any other binner. Running Semibin within Aviary (https://github.com/rhysnewell/aviary/), I noticed that in the binning phase (logging: `SemiBin[22080]...

AroneyS

Long_read problem

1

Hello SemiBin developers, Thank you for the software. It worked well with my nanopore data (R.9.4.1, Guppy v5, super accurate basecalling configuration), until I tried `--sequencing-type=long_read`. Any ideas? Command: ```...

ZarulHanifah

Database Download & Documentation

1

Gday @psj1997 @luispedro and other Semibin developers, Firstly thanks for Semibin(2) - it works amazingly well, so many bins recovered compared to other binning methods :) I want to share...

gbouras13

>It would be great if the user could provide the list of circular contigs to avoid creation of spurious bins. — https://twitter.com/fplazaonate/status/1603366542825119746 > "Circular-aware" binning is a simple but important...

luispedro