coinfinder
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fwhelan
A tool for the identification of coincident (associating and dissociating) genes in pangenomes.
Hello, Thank you for developing coinfinder. According to your publication, about 4 million pairwise tests took 7 minutes with 20 cpu cores. I am running a dataset with 547 genomes...
Dear coin finder devs, We are running coin finder with 1580 genomes and 100 genes (KOs annotated). Follows the command line that we used ``` coinfinder -i $SCRATCH/Coinfinder_analysis/KO_list_COIN.tsv \ -p...
Hi Fiona, I'm getting error messages after trying to run Coinfinder on two different datasets (both of which are small "test" datasets I'm happy to share if required). > ERROR...
Hello! I have recently installed Coinfinder and have been running into issues with getting it to run. Below is the code I am using to run the program. `coinfinder -i...
the gene_p_a outputs of Roary and Panaroo differ enough that I think they justify needing two separate format_ py scripts. Write this for Panaroo's base output and implement a check...
Hi @fwhelan, Just came across the biorXiv manuscript, impressive work! I am working on something similar, but using the OrthoFinder output instead of Roary. Have you considered extending Coinfinder to...
hi again, FYI - you are missing the R dependencies 'flock' and 'future' from the installation instructions on a related note it could be nice if you included a "resume"...
Reading arguments... terminate called after throwing an instance of 'std::logic_error' what(): More than one value for the 'permit_filter' setting has been specified. /tmp/slurmd/job1211360/slurm_script: line 17: 1516483 Aborted (core dumped) coinfinder...
