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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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Use of initialized value in division line 125 #18

Open jennagrimshaw opened 4 years ago

jennagrimshaw commented 4 years ago

Hello, I am running psmc on RADseq data following Liu and Hansen (2017) method that prepares the RADseq data for this psmc analysis. When I run psmc on my full dataset (~1700 scaffolds ranging anywhere from one to in the thousands in length), the analysis works although my bootstraps are all over the place due to the inclusion of many scaffolds with length < 10. When I filter out the small scaffolds (<100), I get this error message:

Use of uninitialized value in division (/) at /psmc/utils/psmc_plot.pl line 125, <> line 195839. Use of uninitialized value in division (/) at /psmc/utils/psmc_plot.pl line 125, <> line 195839. Illegal division by zero at /psmc/utils/psmc_plot.pl line 125, <> line 195839.

I can filter out scaffolds < 5 and it works, but filtering out <10 produces the same error.

Any guidance would be appreciated. I am including the file with all of the scaffolds as well as the file that has been filtered. Thank you, Jenna Grimshaw

15-2.psmcfa.pdf 15-2-long.psmcfa.pdf

Homap commented 4 years ago

Hello,

Did you find any way to solve this problem?

I am running the psmc_plot.pl script and I am getting the same error.

Thank you! Homa

jennagrimshaw commented 4 years ago

No I haven’t! It’s strange because if I filter out < 5, it works fine. But filtering out at <10 produces the error.

On Jul 7, 2020, at 10:34 AM, Homa Papoli notifications@github.com<mailto:notifications@github.com> wrote:

Hello,

Did you find any way to solve this problem?

I am running the psmc_plot.pl script and I am getting the same error.

Thank you! Homa

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Flh3%2Fpsmc%2Fissues%2F18%23issuecomment-654945833&data=02%7C01%7CJenna.grimshaw%40ttu.edu%7C0a5939dbe7ce4279586908d8228b2dda%7C178a51bf8b2049ffb65556245d5c173c%7C0%7C0%7C637297328451465681&sdata=ZdyD7zjV%2BILeFceqv%2Be63OWs6g5NBX3EV42mvCkwrp4%3D&reserved=0, or unsubscribehttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAISXPGYUD3F3L5QKI3Y5PFTR2M56VANCNFSM4OC76FSQ&data=02%7C01%7CJenna.grimshaw%40ttu.edu%7C0a5939dbe7ce4279586908d8228b2dda%7C178a51bf8b2049ffb65556245d5c173c%7C0%7C0%7C637297328451475674&sdata=hkOfKJyzOMezZAr93FLtEJY7vLaIQSQ6wrEt8jkzruc%3D&reserved=0.