PopCOGenT
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philarevalo
Microbial Populations as Clusters Of Gene Transfer
Hello. First all, thanks for this great tool. I'm trying to run this script but a KeyError arrives: Traceback (most recent call last): File "phybreak4.retrieveLikelihood.py", line 142, in ML_dict[subseq][str(tree_no)] +=...
Hello, I was wondering if there's any visualization tool/script you would suggest for plotting the .graphml file generated by PopCOGenT? I'm thinking to make a figure like Figure 3 in...
Hello, I have recently read your article regarding your tool and find it very interesting. However, I have a doubt regarding the expected inputs, because in the publication it is...
Hi, Thanks for this pipeline! I met that issue during the installation and I wonder if that could impact the installation. _conda env create -f PopCOGenT.yml Collecting package metadata (repodata.json):...
Hi, I meet trouble when running `python get_alignment_and_length_bias.py` for about 180 genomes. The following is the error: ``` .Parsing sequences for R2MyF9PMoHcjJAH9 multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File...
Hi, I tried to find the core gene sweep by the test data using PopCOGenT, but I got an error when running phybreak1.generate_maf.py: sh: 1: source: not found 12 genomes...
Hi, We are currently running the core_gene_sweep module, and stuck at third step which is running phyml. Do you have any suggestions on how to make this step run quicker,...
Hi phil，thx a lot for provide this tool But Im running into an error copy pasted below. Traceback (most recent call last): File "get_alignment_and_length_bias.py", line 166, in main() File "get_alignment_and_length_bias.py",...
Can you please create a release (and thus a stable url to a tarball) so that I can try to add `PopCOGenT` to bioconda. See the [bioconda docs](https://bioconda.github.io/contributor/guidelines.html) if you're...
I had run PopCOGenT.sh successfully before, but when I use another dataset it failed, the error message is : Traceback (most recent call last): File "cluster.py", line 315, in main()...
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Microbial Populations as Clusters Of Gene Transfer