Error in hclust(d = d.dist, method = "average") : NA/NaN/Inf in foreign function call (arg 10) about bactaxr

[lmc297]

Hi Tswunami! Thanks so much for using bactaxR (and sorry for not responding sooner!)
I think your issue might be related to the fact that there are not pairwise comparisons for all genomes; for example, if you have 60 genomes, I would expect there to be 60*60 = 3600 ANI values. It looks like there are only 2231 in your data set (I'll try to edit bactaxR to catch this in the future and throw an error)

[Tswunami]

Thank you very much Laura! I have successfully generated the dendrogram using the test dataset provided. I have made sure the input has all pairwise comparison ANI values
However, when trying to run with my actual dataset, I encountered another issue with ANI.dendrogram.

summary (ani)
An object of class bactaxRObject
Number of genomes: 8439
Total number of pairwise ANI comparisons: 71233600
h <- ANI.histogram(bactaxRObject = ani, bindwidth = 0.1)
h
dend <- ANI.dendrogram(bactaxRObject = ani, ANI_threshold = 95, xline = c(4,5,6,7.5), xlinecol = c("#ffc425", "#f37735", "deeppink4", "black"), label_size = 0.5)
Aggregation function missing: defaulting to length
Error: C stack usage 15927104 is too close to the limit

My dataset has a large number of genomes, can I change the limit of the ANI.dendrogram so I can run the package with a larger dataset?

Kind regards

Tswunami

[lmc297]

Hi Tswunami,
8k+ genomes is a lot; I think this is an error due to a lack of memory on whatever machine you're doing (I was unable to replicate this error).
Laura