illegal instruction error on phase_common_static on cow array data

[lholivera]

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 : olivier.delaneau@gmail.com
• 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?

[pettyalex]

What processor are you running this on? This can happen if you run this on a processor that does not support the instructions that Shapeit5 requires, AVX2.

[lholivera]

Thanks a lot!!! It works!!!