search

JosephCrispell / homoplasyFinder

A tool to identify and annotate homoplasies on a phylogeny and sequence alignment
GNU General Public License v3.0
19 stars 3 forks source link

Could not run homoplasyFinder R #24

Open hmamine opened 1 month ago

hmamine commented 1 month ago

Hello, I am trying to run homoplasyFinder (R) on set of whole genome multi-fasta alignment. The file have gaps. I run to the following error. If feedback on the wright way would be helpful. 

> library(library(homoplasyFinder)
> fasta.file<-file.path("multi_ska_out.aln")
> tree.file<-file.path("Bbss_out_gbbins.final_tree.tre")
> inconsistentPositions <- runHomoplasyFinderInJava(treeFile=tree.file, fastaFile=fasta.file,  path="/home/mahassani/Biodata/Boston/v4/")
> Error in .jcheck() : AttachCurrentThread failed! (result:-1)
JosephCrispell commented 1 month ago

Sorry for my slow reply and thanks for giving HomoplasyFinder a go! Do you think you'd be able to share a small example FASTA file that recreates your error and then I can troubleshoot it on my side? You could also try simplifying your FASTA to only include variant positions and/or converting it to a file structure that doesn't include gaps? Thanks again for trying HomoplasyFinder and sorry for my slow reply!