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PengNi / deepsignal2

GNU General Public License v3.0
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FloatingPointError: underflow encountered in exp #11

Open Fatihlrcfs opened 2 years ago

Fatihlrcfs commented 2 years ago

Hi, I am getting this error when ı type "tombo resquiggle singlefast5/ wholegenome.fasta --processes 10 --corrected-group RawGenomeCorrected_000 --basecall-group Basecall_1D_000 --overwrite" ı search on internet but couldnt get solution is there anyone who has the solution. thanks

rowanhowellGE commented 2 years ago

I got a similar error

 File "/opt/conda/lib/python3.9/site-packages/scipy/stats/_continuous_distns.py", line 3820, in _pdf
    return np.sqrt(2.0/np.pi)*np.exp(-x*x/2.0)
FloatingPointError: underflow encountered in exp

This was solved by downgrading scipy to v1.7.3 for me.

Fatihlrcfs commented 2 years ago

hi @rowanhowellGE , sorry for my silly question I did not downgrade my scipy. I tried conda remove/ uninstall and remove scipy package and reinstall again also. Could you say me how did you do it? thansks

rowanhowellGE commented 2 years ago

conda install scipy=1.7.3 should specifically install v1.7.3

Fatihlrcfs commented 2 years ago

Hi @rowanhowellGE ,

I tried but when ı checked the version with "conda list| grep "numpy|scipy" " it shows the version as numpy 1.23.2 and scipy 1.9.0 it was not downgraded?

rowanhowellGE commented 2 years ago

Try removing scipy then try conda install scipy=1.7.3 again?

Fatihlrcfs commented 2 years ago

Hi @rowanhowellGE , I tried removing with conda remove scipy but it says there is no package as scipy. I am confused ..

rowanhowellGE commented 2 years ago

Hmm I think this seems like an issue with conda, rather than deepsignal/tombo.

Fatihlrcfs commented 2 years ago

Hi @rowanhowellGE , yes, it might be ı am going to remove my environment and rebuilt it again. thanks for your time. have a great day.:)