Roary

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installation seem to be stuck

3

I installed all prerequisites to Roary and now I am strying to install the product itself. It seems to be stuck: ``` $ conda install roary Collecting package metadata (current_repodata.json):...

azat-badretdin

When I try to install Roary 3.13.0 in a Conda (Mamba) environment, it works fine when the environment is set at python 3.7, but not in a 3.10 environment (the...

dutchscientist

I have around 300 genome dataset and I am trying to run roary on prokka gff files using 8 threads. Its already more than 10 days that it is running....

MenusGarg

Hi, I encounterd a problem when using roary v3.13.0. I want to perform pan-analysis for Mycoplasma pneumoniae, the number of genes in each of the gff files is about 800,...

Amilycd

Hello, I find that genes with frameshift mutations are often treated as pangenome elements. Is there a way to correct for this? For example, if 32 of 90 strains carry...

sydelstan

Roary grouping genes that don't meet similarity threshold (using `-i 100`, and `-s`)

6

I've been running Roary in order to use the presence/absence tables as input for training ML models (to identify sub-species groups based on shared genomic features). As I don't really...

LijMeh

I got this error; Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl5/5.34/Encode.pm line 70. Anyone with solutions please

charlesshirima

Hi all, I am working on a project that requires creating the alignment of the core genes obtained with Roary. I get the file but it seems the genes are...

BlabOaklandU

Hello, I am using Roary to generate a pan-genome with 682 .gff files obtained from Prokka. The Roary command I'm using is python3 roary_plot.py --label mytree.newick the tree made by...

Ronykumawat