Error executing dnmtools pmd (core dumped) probably related to GSL

[ryansohny]

Error executing dnmtools pmd (core dumped) probably related to GSL

[andrewdavidsmith]

@ryansohny I appreciate that you brought this up. Today we added a check for this in each place where that file format is loaded (6 different commands I think). The error messages aren't great yet, but at least users will be informed of a problem if those values are not in the expected range.

[andrewdavidsmith]

@ryansohny The counts format we use has methylation as fractional. I think you somehow made it into percentages.

https://dnmtools.readthedocs.io/en/latest/counts/

If this turns out to be the only source of your problem, I'll relabel this issue as a need for input validation.

[ryansohny]

Wow this is embarassing. A classic example of "why you should read the manual carefully".
When I created an input from the same sample sequenced in a different way (WGBS), I formatted it in the right way (fractional) so I guess I must have been distracted for some reason.
And I got what I want! It went smoothly.

Thank you very much Professor Smith. Wish you all the best.
Sohn

[ryansohny]

That's great news! Always grateful for developers who go the extra mile to make things easier for their users. Much appreciated it!