emg-viral-pipeline

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Missing process or function with name 'getFileSystem'

3

Missing process or function with name 'getFileSystem'

arpit20328

If a specialized virus metagenome assembly tool should be added to the pipeline to improve initial assemblies, this is something to check more closely https://www.nature.com/articles/s41564-023-01598-2 > COBRA (Contig Overlap Based...

hoelzer

[Feature Request] Conda Distribution for Taxonomic Identification

1

Hi and hope all is well! I wanted to inquire about the conda installation timeline. I know that PPR-Meta is not conda-installable which is why you need to withhold the...

erfanshekarriz

Taxonomic ranks are inverted

11

Hello there! I've been testing the VIRify v2.0 and I realised that the taxonomic annotation on the GFF file has the ranks inverted. For instance: taxonomy=Entomopoxvirinae;Poxviridae;Chitovirales Should be: taxonomy=Chitovirales;Poxviridae;Entomopoxvirinae And...

Ales-ibt

Can Prodigal-GV make 'real world' difference compared to original Prodigal?

2

I am wondering if Prodigal-GV, which incorporates alternative genetic codes tailored to viruses, could be a viable alternative to Prodigal in the Virify pipeline to enhance result accuracy. I am...

GomathiNayagam

preprocess:rename idle state

12

Dears, I'm trying to run a simple test with one of my fasta. But, in the step `preprocess:rename` never ends (11 hours of execution without progress). the log: ``` Launching...

Sanrrone

This issue was discovered during the introduction of the new voting scheme and adjustment of the virus taxonomy: https://github.com/EBI-Metagenomics/emg-viral-pipeline/pull/103 We ran the `assembly.fasta` test file. In the `08-final/gff/assembly_virify.gff` file, we...

hoelzer

The Sankey plot visualization has difficulties when taxonomic ranks are missing. This can be solved to some extent by introducing "unclassified" ranks based on the parent rank. However, this is...

hoelzer

I am running v1.0 on a HPC w/ SLURM and singularity. Apparently, there is a problem in publishing the output of the CheckV step: ```bash WARN: Failed to publish file:...

hoelzer

Bump to 1.0.1 - https://pypi.org/project/checkv/1.0.1/

mberacochea