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fwhelan / coinfinder

A tool for the identification of coincident (associating and dissociating) genes in pangenomes.
GNU General Public License v3.0
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Error: Input phylogeny does not appear to be in newick format. #52

Closed ramadatta closed 1 year ago

ramadatta commented 2 years ago

Hi,

I am trying to input the ML tree in newick format from iqtree tool. But I have the following error:

time ./coinfinder -i gene_presence_absence.csv -p test.newick -o postCoinfinder --associate
Reading arguments...
> CORRECTION ······· = BONFERRONI
> METHOD ··········· = COINCIDENCE
> ALT_HYPOTHESIS ··· = GREATER
> MAX_MODE ········· = ACCOMPANY
> SET_MODE ········· = FULL
> PERMIT_FILTER ···· = NO
> VERBOSE ·········· = NO
> OUTPUT_ALL ······· = NO
> FRACTION CUTOFF ·· = N/A
> SIGNIFICANCE_LEVEL = 0.05
> COMBINED_FILE ···· = gene_presence_absence.csv
> GENE_NAME ······· = Genes
> GENOME_NAME ········ = Genomes
Error: Input phylogeny does not appear to be in newick format.
Exiting...

Please help me if I am missing something. Many thanks in advance.

Datta

sql647 commented 2 years ago

Maybe you can try using FastTree to generate newick files.

rohansmehta commented 2 years ago

I had this same issue and I solved it by installing the packages "getopt" and "ape" in my linux R installation (these are the packages used by the check_newick function). I'm running coinfinder in a wsl environment on my windows machine, so my R packages aren't up to date in the wsl R installation.

fwhelan commented 1 year ago

Closing due to inactivity.