Warnings with example data

[rpensch]

Hi, I have been trying to run PhylogicNDT with the example data as well a my own. Everything seems to work fine, but I am getting runtime warnings (from numpy?) that I can't really explain. I was hoping you might have an idea what is causing them and whether they would affect the output?

These are the warnings I get when using the example data:

/phylogicndt/Cluster/DpEngine.py:591: RuntimeWarning: divide by zero encountered in log
  t1 = sum((np.log(k_prob) * k_prob)[ix])
/phylogicndt/Cluster/DpEngine.py:591: RuntimeWarning: invalid value encountered in multiply
  t1 = sum((np.log(k_prob) * k_prob)[ix])

Edit: This happens both when I run it from the docker and when I install everything manually. I have also tried it on Linux/mac/windows systems. The command I run is the following, taken from the example runs you have provided:

./PhylogicNDT.py Cluster -i Test_Clust -s sample_00:ExampleData/ExampleSamples/MySimulation_0.txt::0.7:0 -s sample_01:ExampleData/ExampleSamples/MySimulation_1.txt::0.7:1 -s sample_02:ExampleData/ExampleSamples/MySimulation_2.txt::0.7:2 -s sample_03:ExampleData/ExampleSamples/MySimulation_3.txt::0.7:3

I did np.seterr(all='raise') and then I get a "FloatingPointError underflow encountered" in DpEngine.py in the function get_gamma_prior_from_k_prior(), specifically in k_prob = stats.gamma.pdf(k_0_map[:, 1], A, scale=1.0 / B) when A and/or B are large numbers.

Some more warnings with my own data:

/phylogicndt/utils/calc_ccf.py:99: RuntimeWarning: invalid value encountered in divide
  subc_ccf_hist /= sum(subc_ccf_hist)
/phylogicndt/Cluster/DpEngine.py:591: RuntimeWarning: divide by zero encountered in log
  t1 = sum((np.log(k_prob) * k_prob)[ix])
/phylogicndt/Cluster/DpEngine.py:591: RuntimeWarning: invalid value encountered in multiply
  t1 = sum((np.log(k_prob) * k_prob)[ix])
/usr/local/lib/python2.7/dist-packages/sklearn/utils/validation.py:429: DataConversionWarning: Data with input dtype float128 was converted to float64 by the normalize function.
  warnings.warn(msg, _DataConversionWarning)
/phylogicndt/data/Patient.py:349: RuntimeWarning: invalid value encountered in greater
  if np.any(mut_coincidence > 0.):
/phylogicndt/BuildTree/Tree.py:277: RuntimeWarning: divide by zero encountered in log
  log_dist = np.log(dist, dtype=np.float64)
/phylogicndt/BuildTree/CellPopulationEngine.py:58: RuntimeWarning: divide by zero encountered in log
  log_dist = np.log(dist, dtype=np.float32)

[ipstone]

I am encountering the same error