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Hello! First, thank you for this tool - it's been quite helpful to me in the past! However, as of about a month ago the NCBICDD1000 tool has stopped working for larger genomes, even genomes I've annot…
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Using a masked genome and getting a few of these warning messages from Augustus when being used from within BUSCO
```
WARNING: The following job was killed as it was taking too long (>1hr) to comp…
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When using `datasets` to download a large collection of genomes, many of the associated ```.fna``` files are silently truncated. I was fortunate in that: 1) a few of the files were truncated so that…
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Hello --
Thank you so much for making an accessible genome finishing tool. I've greatly enjoyed running the pipeline, and it was wonderfully easy to install and run. I did want to ask about one iss…
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I'm trying to run PHIST on a single viral contig vs a large database of gzipped bacterial genomes. The program finishes without errors, but stops after the first ~715 reference genomes and reports the…
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As stated in [diamond.py](https://github.com/chklovski/CheckM2/blob/d40aef910f24bf7e479e5f7ff1ed326f30d2884b/checkm2/diamond.py):
> Diamond only accepts single inputs, so we concat protein files a…
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Hello,
Our lab has been using hifiasm for a number of genome assembly projects. We are using Nanopore reads (kit 14 chemistry, R10.4.1 flow cells) that have been error-corrected with PECAT or HERRO…
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Hi,
As mentioned in the manual, "HaploMerger2 is not suitable to work on the assemblies with a scaffold N50 size N50>50Kb; it works better when the scaffold
N50>100Kb; and it works much better wh…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
3.8.10 (default, Nov 22 2023, 10:22:35)
CPython
Linux-6.0.12-76060012-generic-x86_6…
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Hi, thank you for this approach, absolutely fascinating! I'm hoping to use this in a workflow to assess and triage eukaryotic genome annotations using FoldSeek. The range of protein sequences can be s…