segmentation fault error in Sequoia about sequoia

[JiscaH]

Oops! That shouldn't happen obviously. How many individuals & SNPs are in the dataset? I will make a mock dataset tomorrow (European time) to see if I can reproduce the issue.

You could try the following options when running sequoia():

• FindMaybeRel = FALSE (if you changed the default)
• CalcLLR = FALSE (although I don't think the problem lies there)
• quiet = 'verbose' (to get more detail on where exactly the crash is happening)

I assume this is sequoia version 1.3.3, as on CRAN? Version 1.3.6 on here may or may not have the same issue, but I don't have access to a Mac to compile it for you.

Cheers,
Jisca

[walla296]

Hi Jisca, Thanks for the quick response and suggestions- I¹ll try them now. I have 2,549 individuals and 557 SNPs in the file. Cheers, Liz From: JiscaH <[email protected]> Reply-To: JiscaH/sequoia <[email protected]> Date: Thursday, February 6, 2020 at 12:48 PM To: JiscaH/sequoia <[email protected]> Cc: Elizabeth Wallace <[email protected]>, Author <[email protected]> Subject: Re: [JiscaH/sequoia] segmentation fault error in Sequoia (#7) Oops! That shouldn't happen obviously. How many individuals & SNPs are in the dataset? I will make a mock dataset tomorrow (European time) to see if I can reproduce the issue. You could try the following options when running sequoia(): * FindMaybeRel = FALSE (if you changed the default) * CalcLLR = FALSE (although I don't think the problem lies there) * quiet = 'verbose' (to get more detail on where exactly the crash is happening) I assume this is sequoia version 1.3.3, as on CRAN? Version 1.3.6 on here may or may not have the same issue, but I don't have access to a Mac to compile it for you. Cheers, Jisca � You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#7?email_source=notifications&email _token=AHGRAKV6SAYDNY7WSLLXNCTRBRENBA5CNFSM4KRA7BV2YY3PNVWWK3TUL52HS4DFVREXG 43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELAEOHI#issuecomment-583026461> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHGRAKRWKTMJTGBKQDQKGBTRB RENBANCNFSM4KRA7BVQ> . [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "#7?email_source=notifications\u0026 email_token=AHGRAKV6SAYDNY7WSLLXNCTRBRENBA5CNFSM4KRA7BV2YY3PNVWWK3TUL52HS4DF VREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELAEOHI#issuecomment-583026461", "url": "#7?email_source=notifications\u0026 email_token=AHGRAKV6SAYDNY7WSLLXNCTRBRENBA5CNFSM4KRA7BV2YY3PNVWWK3TUL52HS4DF VREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELAEOHI#issuecomment-583026461", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

[JiscaH]

Hello Liz,
I've used dataset of that size & larger on many occasions (up to 6000 indiv), so that in itself can't be the cause of the problem!

If at all possible, could you email the data to jisca.huisman @ gmail.com ? Needless to say I'll treat the data confidentially.

Jisca

[walla296]

Okay, thanks. Just sent you the data file. The original run parameters were: MaxSibIter = 10, MaxMismatch = 10, UseAge = "yes", FindMaybeRel = TRUE, CalcLLR = TRUE, quiet = FALSE.
After changing to FindMaybeRel = FALSE, CalcLLR = FALSE , quiet = 'verbose', as you suggested, RStudio still aborted the session. the following was displayed just before the crash:
Round 2 start
Finding pairs...
Clustering...
Merge clusters...
Sibship parent replacement...
Grow clusters...