gubbins

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How to know the specific regions that were extracted by Gubbins

3

Rathanin-github

I have run gubbins installed on Debian 9.9 with `apt`, using the following command: `run_gubbins -v -n -p test_thing_cl3act -c 8 ../../mm2b_act_cl3.aln.fa > gubbins.log &` Is this possibly because the...

nzmacalasdair

some questions about the file ".filtered_polymorphic_sites.fasta"

4

The description of this file is "FASTA format alignment of filtered polymorphic sties used to generate the phylogeny in the final iteration" (1) what "filtered" means? It filtered the recombination...

zhaoxvwahaha

Hi, How can I get the specific position for each recombination events, I found that "maskrc-svg" could help to extract the position, but I wonder, any output file of Gubbins...

zhaoxvwahaha

Midpoint rooting problem

7

Hi all, I'm using Gubbins to estimate r/m for sequence clusters, and it really works smoothly and splendidly. It's just that – unlike stated on Github – it doesn't return...

rmostowy

Core dumped segmentation fault (with 2.3.1 and 2.3.4)

1

Hello, I know there are some thread about apparent memory issues. So far, I run gubbins on 50 genomes + a ref on Intel Xeon (32 apparent cores) and 62GB...

sbridel

install gubbins

6

I failed to install gubbins using Conda and Homebrew as follows. Any comments would be greatly appreciated. ### Conda ``` $conda install gubbins Solving environment: failed UnsatisfiableError: The following specifications...

haruosuz

Gubbins can't find dendropy

2

I am trying to run gubbins on an alignment from snippy (have tried v3, with python3.5, and v4, with python 3.6) however I keep getting an error saying "no module...

CJREID

SNP counts on branches

2

In the final_tree.tre output file produced by Gubbins, the branch labels that should be SNP counts are decimal numbers instead which don't match the numbers in the per_branch_statistics.csv file. Could...

nwheeler443

Run a screening test to reject alignments that will likely crash

1

The `iqtree` tool runs a simple "composition test" on any alignment you give it, and then complains if it is *too simple*. What you want is the negative version of...

tseemann