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odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool
MIT License
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free(): invalid pointer \n Aborted (core dumped) #54

Open Bennouhan opened 3 years ago

Bennouhan commented 3 years ago

Hi, I'm getting a shapeit4 issue during the first burn-in iteration

g++ Version:

$g++ --version g++ (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0 Copyright (C) 2019 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Log:

SHAPEIT

  • Author : Olivier DELANEAU, University of Lausanne
  • Contact : olivier.delaneau@gmail.com
  • Version : 4.2.0
  • Run date : 09/04/2021 - 16:29:32

Files:

  • Input VCF : [../data/unphased/11/HGDP_1000g_regen_no_AT_CG_3pop_geno05_11.vcf.gz]
  • Reference VCF : [../data/reference/shapeit4/CCDG_14151_B01_GRM_WGS_2020-08-05_chr11.filtered.shapeit2-duohmm-phased_header.vcf.gz]
  • Genetic Map : [../data/gen_maps/chr11.b38.gmap.gz]
  • Output VCF : [../data/phased/11/HGDP_1000g_regen_no_AT_CG_3pop_geno05_shapeit4_11.vcf.gz]

Parameters:

  • Seed : 15052011
  • Threads : 16 threads
  • MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
  • PBWT : Depth of PBWT neighbours to condition on: 4
  • PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.02 cM]
  • HMM : K is variable / min W is 2.50cM / Ne is 15000
  • HMM : Recombination rates given by genetic map
  • HMM : AVX2 optimization active

Initialization:

  • VCF/BCF scanning [Nm=1690 / Nr=3202 / L=1018000 / Reg=11] (602.40s)
  • VCF/BCF parsing [Hom=92.8% / Het=7.2% / Mis=0.0%] (679.11s)
  • GMAP parsing [n=168609] (0.26s)
  • cM interpolation [s=103172 / i=914828] (0.07s)
  • Region length [134943857 bp / 158.3 cM]
  • HMM parameters [Ne=15000 / Error=0.0001 / #rare=144758]
  • PBWT indexing [l=7812] (0.05s)
  • HAP update (10.39s)
  • H2V transpose (32.16s)
  • PBWT phase sweep (107.38s)
  • Build genotype graphs [seg=41377137] (2.59s)

Burn-in iteration [1/5]

  • V2H transpose (2.14s)
  • PBWT selection (35.48s)
  • C2H transpose (0.31s)
  • HMM computations [K=389.134+/-196.794 / W=4.14Mb] (329.76s) free(): invalid pointer Aborted (core dumped)

Thanks a lot, Ben

anailis commented 3 years ago

I also had this issue with v. 4.2.0 downloaded from Conda (only thing in a fresh env), although mine did not occur until a later burn-in iteration. I downgraded to 4.1.0 and no longer had this issue.

odelaneau commented 3 years ago

Please install v4.2.1 instead of v4.2.0 to solve this issue.

Best,