RuntimeWarning: invalid value encountered in sqrt

[ghost]

Hi @AliciaSchep ,

Nucleoatac is currently running (25hrs) and the output below shows a warning (step 1) and an error (step 3). Are these going to be a problem? Does the run need to be stopped to fix the cause of the error and warning? Will the results still be reliable? What is causing these and how do you think I can fix them (if that is what is needed)?

Thank you,
Kenneth

Command run:

nucleoatac run --bed final.broadPeak --bam mgwatd2.bam --fasta ref_mm10.fasta --out mgwatd2 --cores 16

nucleoatac version 0.3.4

start run at: 2017-04-07 15:31
---------Step1: Computing Occupancy and Nucleosomal Insert Distribution---------
/usr/lib64/python2.7/site-packages/matplotlib/collections.py:526: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
if self._edgecolors == 'face':
Making figure
---------Step2: Processing Vplot------------------------------------------------
---------Step3: Obtaining nucleosome signal and calling positions---------------
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)
/usr/lib/python2.7/site-packages/nucleoatac/NucleosomeCalling.py:86: RuntimeWarning: invalid value encountered in sqrt
return np.sqrt(var)

[AliciaSchep]

This might be the same issue as #55, which I still haven't figure out how to fix :/ You could try running the example