I was trying to run BactDating on my Klebsiella tree and am getting the error.
I generated core-genome alignment using panaroo and snp-sites to get only the variants' alignment.
Then I generated the iqtree using this command
iqtree -s core_gene_alignment.variants_only.fas -m GTR+G -alrt 1000 -bb 1000 -nm 200 -nt AUTO -ntmax 40 -czb
Here are the contents from my Rscript where I am trying to run the Bactdating
t=read.tree('~/Downloads/core_gene_alignment.variants_only.fas.treefile')
t1 <- midpoint_root(t)
sum(t1$edge.length)
t1$edge.length=t1$edge.length*37158
#write the node ids to get the dates in same order
ids <- t1$tip.label
write.csv(ids,"~/Downloads/ids_180.csv")
d=read.csv("~/Downloads/dates_180.csv",header = FALSE)
d1 <- as.vector(t(d))
#find the root to tip analysis to find MRCA
rttip =roottotip(t1,d1)
#build the time tree
res=bactdate(t1,d1)
and I get this error
Error in if (log(runif(1)) < l2 - l + dgamma(mu2, shape = 0.001, scale = 1000, : missing value where TRUE/FALSE needed
There are several problems that can trigger this message.
You should make sure that your input tree has no branches of negative length, and also no polytomies.
Hi,
I was trying to run BactDating on my Klebsiella tree and am getting the error.
I generated core-genome alignment using panaroo and snp-sites to get only the variants' alignment. Then I generated the iqtree using this command
iqtree -s core_gene_alignment.variants_only.fas -m GTR+G -alrt 1000 -bb 1000 -nm 200 -nt AUTO -ntmax 40 -czb
Here are the contents from my Rscript where I am trying to run the Bactdating
and I get this error
Error in if (log(runif(1)) < l2 - l + dgamma(mu2, shape = 0.001, scale = 1000, : missing value where TRUE/FALSE needed
Please help me out.