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I've been compling a list of phage tools for something I'm writing and came across this GitHub. This looks really exciting and I look forward to trying this out.
I think there might be some tools …
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* pharokka version: 1.5.1
* Python version: 3.10.13
* Operating System: linux
### Description
Dear George,
Thank you for pharokka! We have it running overall well but we're getting some conti…
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Hi,
I used geNomad to identify viruses in addition to VirSorter2 and Cenote-taker2. Subsequently, I used geNomad's annotate module to assign taxonomy to all viral contigs, including those identifie…
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Hi Mike,
Thank you for Cenote-Taker2! However, I am facing a problem when i run the commond:
This is my code: python /media/home/user05/anaconda3/envs/cenote-taker2/bin/run_cenote-taker2.0.1.py --co…
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I've been running Cenote Taker2 on a single sample, and it's been stuck on the PHANOTATE step for a bit over 24 hours now, without any visible update or running process.
When I run `ps -a` I see th…
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This is less of a specific bug, and more something that would be helpful to change a bit.
I have noticed that when some step in the pipeline fails, it isn't entirely obvious at the end when looking…
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Hi all,
I am using version 2.1.2 and I do not know if this was corrected in newer versions. When I search for circular genomes assembled with De Bruijn Graph based assembler I expect to find a dup…
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hi Mike,
I met the same as Issue #22. I install krona with mamba. Then I successfully updated the Kron database using the following code.
KRONA_DIR=$( which python | sed 's/bin\/python/opt\/kro…
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Dear, developers
During unpacking, the following error occurs.
```
2022-01-26 05:04:08 (1.72 MB/s) - ‘pdb70_from_mmcif_latest.tar.gz’ saved [23794671727/23794671727]
md5sum
pdb70_a3m.ffdata
…
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When I run `python ~/software/Cenote-Taker2/Cenote-Taker2/run_cenote-taker2.py -c AsianEle01.fa -r AsianEle01_ct.out -m 32 -t 32 -p True -db virion --minimum_length_linear 3000 --lin_minimum_hallmark_…