Error in merge.clone.trees

[kxxxjo]

Hi,

First of all, thanks for distributing the software.

I generated the input for clonevol using pyclone-vi and ran the 'infer tree' process of the clonevol, but the following error message occurred.

# infer tree
> y = infer.clonal.models(variants = input,
                         cluster.col.name = 'cluster',
                         vaf.col.names = vaf.col.names,
                         sample.groups = NULL,
                         cancer.initiation.model='monoclonal',
                         subclonal.test = 'bootstrap',
                         subclonal.test.model = 'non-parametric',
                         num.boots = 1000,
                         founding.cluster = 1,
                         cluster.center = 'mean',
                         ignore.clusters = NULL,
                         clone.colors = NULL,
                         min.cluster.vaf = 0.01,
                         sum.p = 0.05,
                         alpha = 0.05)
Sample 1: ADK <-- ADK
Sample 2: NET <-- NET
Using monoclonal model
Note: all VAFs were divided by 100 to convert from percentage to proportion.
Generating non-parametric boostrap samples...
ADK : Enumerating clonal architectures...
Determining if cluster VAF is significantly positive...
Exluding clusters whose VAF < min.cluster.vaf=0.01
Non-positive VAF clusters: 1,4,5,3,2 
ADK : 1 clonal architecture model(s) found

NET : Enumerating clonal architectures...
Determining if cluster VAF is significantly positive...
Exluding clusters whose VAF < min.cluster.vaf=0.01
Non-positive VAF clusters: 4,2,1,3,5 
NET : 1 clonal architecture model(s) found

Finding consensus models across samples...
Found  1 consensus model(s)
Generating consensus clonal evolution trees across samples...
Error in merge.clone.trees(m, samples = samples, sample.groups, merge.similar.samples = merge.similar.samples) : 
  ERROR: Something wrong. No clones left after filter. They might have been excluded.

I had just two samples (ADK and NET) and I attached input file for clonevol. 20220207_clonevol_input_github.txt

Please let me know why this error occurred.

Thanks!

[Yunuuuu]

Same problem

[adhisadi]

I changed the "min.cluster.vaf = 0.01" to "min.cluster.vaf = 0" and then it worked. I might be wrong though