RuntimeWarning: overflow encountered in power

[mfas7]

Hi!

Thanks for creating such a useful tool! We've encountered a problem and after reading through the issues posted on Github that might be related to this problem and trying some suggestions to fix this (like changing the size of the bed file), we are still having trouble. Below is the code I enter and the error that pops up.

Any insight/help would be greatly appreciated!

Thanks so much!

nucleoatac run --bed shortened2.bed --bam ATAC_Liver_L1A_GSM2147562_sort.bam --fasta mm10.fa --out test --cores 4
Command run: /Users/fasolino/NucleoATAC/venv/bin/nucleoatac run --bed shortened2.bed --bam ATAC_Liver_L1A_GSM2147562_sort.bam --fasta mm10.fa --out test --cores 4
nucleoatac version 0.3.2
start run at: 2016-11-15 11:28
---------Step1: Computing Occupancy and Nucleosomal Insert Distribution---------
/Users/fasolino/NucleoATAC/venv/lib/python2.7/site-packages/nucleoatac/Occupancy.py:45: RuntimeWarning: overflow encountered in power
res[nz] = a * x_mod[nz]**(k-1) * np.exp(-x_mod[nz]/theta) / (theta **k * gamma(k))
Making figure
---------Step2: Processing Vplot------------------------------------------------
/Users/fasolino/NucleoATAC/venv/lib/python2.7/site-packages/pyatac/VMat.py:100: RuntimeWarning: invalid value encountered in divide
tmp1 = self.mat / np.sum(self.mat)
---------Step3: Obtaining nucleosome signal and calling positions---------------
/Users/fasolino/NucleoATAC/venv/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:280: RuntimeWarning: invalid value encountered in less
self.smoothed.vals[ self.smoothed.vals < 0] = 0
---------Step4: Making combined nucleosome position map ------------------------
---------Step5: Calling NFR positions-------------------------------------------
end run at: 2016-11-15 11:28

[AliciaSchep]

Are any figures generated from Step 1? If so, if you can post them, those can be useful diagnostic (sometimes there are errors because fragment size is really different from what is expected. ideally the script would flag this and give a meaningful message)