Floating point error in NanoSplicer.py

[sagnikbanerjee15]

Hello,

I am trying to execute the commands in scripts.sh. The first two commands were executed without any error. The last command gives the following error.

python3 ../bin/NanoSplicer.py -i example.bam -f fast5s/ -r sequins_genome.fa JWR_subset.h5
Traceback (most recent call last):
  File "/NanoSplicer/examples/../bin/NanoSplicer.py", line 65, in <module>
    from tombo import tombo_helper, tombo_stats, resquiggle
  File "/opt/conda/lib/python3.10/site-packages/tombo/tombo_stats.py", line 84, in <module>
    HALF_NORM_EXPECTED_VAL = stats.halfnorm.expect()
  File "/opt/conda/lib/python3.10/site-packages/scipy/stats/_distn_infrastructure.py", line 2949, in expect
    dub = integrate.quad(fun, d, ub, **kwds)[0]
  File "/opt/conda/lib/python3.10/site-packages/scipy/integrate/_quadpack_py.py", line 463, in quad
    retval = _quad(func, a, b, args, full_output, epsabs, epsrel, limit,
  File "/opt/conda/lib/python3.10/site-packages/scipy/integrate/_quadpack_py.py", line 577, in _quad
    return _quadpack._qagie(func,bound,infbounds,args,full_output,epsabs,epsrel,limit)
  File "/opt/conda/lib/python3.10/site-packages/scipy/stats/_distn_infrastructure.py", line 2926, in fun
    return x * self.pdf(x, *args, **lockwds)
  File "/opt/conda/lib/python3.10/site-packages/scipy/stats/_distn_infrastructure.py", line 2102, in pdf
    place(output, cond, self._pdf(*goodargs) / scale)
  File "/opt/conda/lib/python3.10/site-packages/scipy/stats/_continuous_distns.py", line 3956, in _pdf
    return np.sqrt(2.0/np.pi)*np.exp(-x*x/2.0)
FloatingPointError: underflow encountered in exp

Could you please look into this?

Thank you.

[youyupei]

Hi @sagnikbanerjee15,

Sorry for the late reply. Based on your error message, it seems the error happened when NanoSplicer was trying to import tombo.stats. Would you be able to check whether you could start a new python3 session and run from tombo import tombo_stats? If not, I would suggest re-install tombo.

Regards,
Yupei