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Hi!
I have 921 eukaryotic genome assemblies - from NCBI and literature - I would like to run ContScout on with nr as the database.
Running 5 assemblies initially, 2 completed successfully (run …
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Hi,
I tried to run eggnog-mapper/2.1.6
`emapper.py --cpu 0 -m mmseqs --itype metagenome --mmseqs_db ~/ku_00039/people/dinghe/eggNOG_mapperDB/mmseqs -i scaffolds.fasta -o eggNOG_mapper_out`
And …
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I hope to access the data link mentioned in your paper, https://plass.mmseqs.com, but I was redirected to this Git repository. Is the data still accessible?
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Hello, I'm trying to run openfold multimer inference on some fasta files I have. I've been using the collabfold databases to generate the sequence alignments as these are smaller than the AF2 database…
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For the previous problem, I modified the mmseq.py file and changed it to：
if mmseqs_profiles_url is None:
mmseqs_profiles_url = 'file:///xxxx/PlasX_mmseqs_profiles.tar.gz'
if coefficients_url is…
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I'm trying to use a clustered version of the NR database for taxonomy assignment but am running into some issues. Any assistance would be appreciated.
## Expected Behavior
When running `mmseqs cre…
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* pharokka version:1.4 & 1.5.1
* Python version: Python 3.10.8
* Operating System: Rocky Linux 8.7 (Green Obsidian)
### Description
Hi @gbouras13, When trying to run pharokka_proteins.py in a se…
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* pharokka version: 1.6.0
* Python version: 3.10.8
* Operating System: Ubuntu 20.04
Hello,
Pharokka is very promising for annotating viral genomes. However, when I tried to run it with my data…
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Dear all
We are currently testing AGNOSTOS on our system, but breaking it based on the different snakemake sub-runs in `agnostos-wf/db_update/rules/`
In the steps within mmseqs_clustering_update…
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Hi,
We have installed Agnostos-wf and in our first attempt to analyze our metagenomic data we got the error bellow (in bold) after running 'db_creation' workflow
Used command line:
_snakem…