B. longum database, error "invalid value encountered in double_scalars"

[rthielemann]

Hello,

thanks for providing this tool! I used the provided B. longum database to test the presence of B. longum strains in metagenomic samples. After running the strainest est command on a single sample against the database, results were output as expected but the script terminated with the following error:

/usr/lib/python2.7/dist-packages/scipy/stats/stats.py:3029: RuntimeWarning: invalid value encountered in double_scalars
  r = r_num / r_den

The info.txt looked like this

Filename	MinDepth	MaxDepth	NPos	NGen	Alpha	MSEAve	MSEStd	NLassoIter	R	PVal
probioticMappedBifido.sorted.bam	8.0	22.0	63996	1	0.009529665531520763	0.0006187400807969682	8.779356743394051e-05	2	nan	1.0

In the results directory, the abund.txt, max_ident.txt, counts.txt, info.txt, and mse.pdf files were produced as expected.

How should I interpret this error message?

[alimayy]

@rthielemann I think I had this too when one of the strains in the db had 0 abundance. Can it be that?