Error with some rsIDs

[jcmarca]

Postgap fails when using specific variations in a summary file

Here is an example of a summary file including one of the failing rsID:

variant_id beta p-value
rs2862954 -0.0291 2.00E-10

And this is the error message shown in the log file:

~/postgap/lib/postgap/Finemap.py:803: RuntimeWarning: divide by zero encountered in log
return subset_size*numpy.log(p) + (m - subset_size)numpy.log(1-p)
~/postgap/lib/postgap/Finemap.py:803: RuntimeWarning: invalid value encountered in double_scalars
return subset_sizenumpy.log(p) + (m - subset_size)numpy.log(1-p)
~/postgap/lib/postgap/Finemap.py:803: RuntimeWarning: invalid value encountered in multiply
return subset_sizenumpy.log(p) + (m - subset_size)*numpy.log(1-p)

[dzerbino]

Hello @jcmarca ,

I hope you are doing well!

Could you please confirm which commit you are working off at the moment?

Cheers,

Daniel

[jcmarca]

Hi Daniel. I’m doing well, thank you. I hope you are fine too. I’m working in the Master branch updated until the last commit. Commit f82a3ad "Bump ipython from 6.2.1 to 7.16.3 in /tests” Best, Jose.

…

On 3 May 2022, at 19:57, Daniel Zerbino ***@***.***> wrote: Hello @jcmarca <https://github.com/jcmarca> , I hope you are doing well! Could you please confirm which commit you are working off at the moment? Cheers, Daniel — Reply to this email directly, view it on GitHub <#180 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC6TF4EWHPIPN7PDQAYFFVTVIFZI5ANCNFSM5U6RHSBA>. You are receiving this because you were mentioned.