Assertion generated at shapeit4: src/phaser/phaser_algorithm.cpp:50

[mdkeehan]

Hi,

Thanks for writing such a good tool and making it MIT licensed. We have been evaluating shapeit4 on low density cattle snp chip data and a colleague has been generating the following assertion.

shapeit4: src/phaser/phaser_algorithm.cpp:50: void phaser::phaseWindow(int, int): Assertion `threadData[id_worker].Kvec[w].size()>0' failed.
Aborted (core dumped)

The command line we have been using is

shapeit4 --really.simple.ped.phased.vcf.gz --map  1cmMb.map -O  out.vcf -R Chr5 --thread 4  -W 20000000 --effective-size 400  --pbwt-disable-init --mcmc-iterations  6b,1p,2b,1p,2b,20m

The input vcf has 1935 markers ranging over Chr5 which (in cattle) is 121 MB long. So with -W 20,000,000 we have 6 windows with 400 markers per window.

By experimenting with the parameters I have found setting -W to 200,000,000 i.e force 1 window over the chromosome the command completes.

Is there a recommended minimum number of markers per window?

[odelaneau]

Looking at the assert, it's definitely related to the low density of variants. But It's a tricky problem to solve with few info. I am happy to look at this in more details if you could send me a small example dataset repoducing the error.

Cheers,

[mdkeehan]

Hi Olivier,

Thanks for responding. It will be difficult for me to release a public dataset plus given that we have a work around i.e. to use longer windows I won’t be following this up furthur. Please mark the bug as closed.

Mike

From: Olivier Delaneau notifications@github.com Sent: Friday, 22 February 2019 9:15 PM To: odelaneau/shapeit4 shapeit4@noreply.github.com Cc: Michael Keehan Michael.Keehan@lic.co.nz; Author author@noreply.github.com Subject: Re: [odelaneau/shapeit4] Assertion generated at shapeit4: src/phaser/phaser_algorithm.cpp:50 (#1)

Looking at the assert, it's definitely related to the low density of variants. But It's a tricky problem to solve with few info. I am happy to look at this in more details if you could send me a small example dataset repoducing the error.

Cheers,

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