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illegal instruction error on phase_common_static on cow array data

Open lholivera opened this issue 11 months ago • 2 comments

Hi I'm trying to run phase_common_static on my cow array data, and blocked with this error: phase_common_static --region 1 -I huellas.vcf.gz -O huellas_prueba.bcf --log log.txt -T 8

[SHAPEIT5] phase_common (jointly phase multiple common markers)

  • Author : Olivier DELANEAU, University of Lausanne
  • Contact : [email protected]
  • Version : 5.1.1 / commit = 990ed0d / release = 2023-05-08
  • Run date : 22/03/2024 - 14:32:28

Files:

  • Input : [huellas.vcf.gz]
  • Output : [huellas_prueba.bcf]
  • Output format : [bcf]
  • Output LOG : [log.txt]

Parameters:

  • Seed : 15052011
  • Threads : 8 threads
  • MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
  • PBWT : [window = 4cM / depth = auto / modulo = auto / mac = 5 / missing = 0.1]
  • HMM : [window = 4cM / Ne = 15000 / Constant recombination rate of 1cM per Mb]

Reading genotype data:

  • VCF/BCF scanning done (0.07s)
    • Variants [#sites=3098 / region=1]
      • 22 sites removed in main panel [multi-allelic]
    • Samples [#target=163 / #reference=0]
  • VCF/BCF parsing done (0.07s)
    • Genotypes [0/0=52.040%, 0/1=36.578%, 1/1=10.923%, ./.=0.459%, 0|1=0.000%]

Setting up genetic map:

  • Region length [158183640 bp / 158.2 cM (assuming 1cM per Mb)]
  • HMM parameters [Ne=15000 / Error=0.0001 / #rare=0]

Initializing data structures:

  • Impute monomorphic [n=0] (0.00s)
  • HAP update (0.01s)
  • H2V transpose (0.00s)
  • PBWT parameters auto setting : [modulo = 0.022 / depth = 7]
  • PBWT initialization [#eval=3082 / #select=2697 / #chunk=28] (0.01s)
  • PBWT phasing sweep (0.02s)
  • Build genotype graphs [seg=61622] (0.01s)

Burn-in iteration [1/5]

  • PBWT selection (0.07s) Instrucción ilegal (`core' generado)

I've changed parameters on PBWT (almost all combinations), filtered samples and snps, read source code, etc, without luck. Any ideas?

lholivera avatar Mar 22 '24 17:03 lholivera