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JiscaH / sequoia

R package for pedigree inference based on SNP data
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segmentation fault error in Sequoia #7

Closed walla296 closed 4 years ago

walla296 commented 4 years ago

Hi, I'm running a large dataset in sequoia that is exiting with the following error: Sibships - Initial Total LL : [1] -232355 Round 01 end, Total LogLik: [1] -228607.6 No. dams, sires (incl. dummies): [1] 362 362

caught segfault address (nil), cause 'unknown'

Traceback: 1: SeqParSib(ParSib = "sib", Specs = Specs, GenoM = GenoM, LhIN = LifeHistData[, 1:3], AgePriors = Ag$ 2: sequoia(GenoM = GenoM, LifeHistData = LH, MaxSibIter = 10, MaxMismatch = 10, UseAge = "yes", FindM$ An irrecoverable exception occurred. R is aborting now ... /var/spool/slurmd/job34109895/slurm_script: line 25: 164736 Segmentation fault (core dumped) Rscript $

Other, smaller, data files complete normally. I have reproduced this error across R console v3.5.1 and RStudio v1.1.456 on my MAC running Sierra, as well as on an HPC. In all cases, the package runs normally most of the way through the analysis before exiting with the seg fault error. Hoping to find a fix for this, thanks for any suggestions!

JiscaH commented 4 years ago

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():

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 commented 4 years ago

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 notifications@github.com Reply-To: JiscaH/sequoia reply@reply.github.com Date: Thursday, February 6, 2020 at 12:48 PM To: JiscaH/sequoia sequoia@noreply.github.com Cc: Elizabeth Wallace walla296@umn.edu, Author author@noreply.github.com 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():

Cheers, Jisca

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JiscaH commented 4 years ago

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 commented 4 years ago

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...