PopCOGenT

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Core gene sweeps module

9

Hi, thanks a lot for providing this excellent software, very useful! I’d have a few questions about the core_gene_sweeps module. Hope it’s ok that I put them together in one...

thr44pw00d

failed job run_mmseqs

5

Hi phil@philarevalo I meet a problem when running "bash snakefile.sh" in flexible_genome_sweeps. the following is the error. Waiting at most 5 seconds for missing files. MissingOutputException in line 88 of...

jiyunli

Changes: 1. new snakemake module style: 1. specify input via `ls *.fa > genome.fasta.ls` 2. import "src/PopCOGenT/PopCOGenT.smk" as a module with params specified 3. expect output: `genome-length_bias-0.000355362.cluster.tsv` 2. update python...

Hocnonsense

Hi, popcogenT is excellent software and we have used it to resolve many questions. However, one situation we meet is that we have gradually increased our genome set. When the...

444thLiao

Hi Team, I am facing the following issue **[[file not found error](https://github.com/philarevalo/PopCOGenT/files/12775811/Popcogent_issue.txt)]** while executing the PopCOGenT tool on around 361 gene sequences. I was able to run the tool on...

Balu-Anupoju-Vt

Core Gene Sweeps phybreak_parameters.txt clarification

2

Hello, I am unclear on the parameter inputs. What is the difference between input_contig_dir and contig_dir and how do these relate to the input genomes dir for PopCOGenT? What are...

rotheconrad

Hi, I want to extract the sequences based on the output of `*.core_sweeps.csv`, which provided the start and end positions. In the `README`, you mentioned that > `*.core_sweeps.csv`: The positions...

Xiaojun928

Python 3 pachage rpy2 needs to be installed to use the R function.

7

Hi, still having trouble running flexible_genome_sweeps (bash snakemake.sh). After setting the configuration file and running the script I get this error: Provided cores: 1 Rules claiming more threads will be...

rsiani

The flexible gene sweep pipeline should have a test output to check against.

philarevalo

PopCOGenT

9

Im running into an error copy pasted below. I am running PopCOGenT on 3 assemblies Ouput directory does not exist. Creating new directory. Traceback (most recent call last): File "/GWSPH/groups/liu_price_lab/tools/anaconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py",...

malihaaziz