Haploid underflow impossible to recover for [sample]

[LimKaiShi]

Hi, I am running phasing using phase_common_static 5.1 version. But I kept running into the problem of haplotype underflow...

This is the code that i run

%%bash
WORK_DIR='/home/jupyter/LRRK2/CHI/r10_hap'
cd $WORK_DIR

./phase_common_static \
--input merged_CHI_LRRK2_no_dup_renamed_filtered.vcf.gz \
--region chr12 \
--map plink.chr12.GRCh38.edit_shapeit.map \
--output noref_shapeit_phased_merged_CHI_LRRK2_no_dup.vcf 

here is my complete log output

SHAPEIT5] phase_common (jointly phase multiple common markers)
  * Author        : Olivier DELANEAU, University of Lausanne
  * Contact       : olivier.delaneau@gmail.com
  * Version       : 5.1.0 / commit = 492781e / release = 2023-04-13
  * Run date      : 29/11/2024 - 03:32:27

Files:
  * Input         : [merged_CHI_LRRK2_no_dup_renamed_filtered.vcf.gz]
  * Genetic Map   : [plink.chr12.GRCh38.edit_shapeit.map]
  * Output        : [noref_shapeit_phased_merged_CHI_LRRK2_no_dup.vcf]
  * Output format : [bcf]

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 / Recombination rates given by genetic map]

Reading genotype data:
  * VCF/BCF scanning done (0.01s)
      + Samples [#target=951 / #reference=0 / #sites=27 / region=chr12]
      + 14 sites removed in main panel [multi-allelic]
  * VCF/BCF parsing done (0.01s)
      + Genotypes [0/0=71.535%, 0/1=22.643%, 1/1=5.822%, ./.=0.000%, 0|1=0.000%]

Setting up genetic map:
  * GMAP parsing [n=165326] (0.07s)
  * cM interpolation [s=0 / i=27] (0.00s)
  * Region length [140917 bp / -nan cM]
  * HMM parameters [Ne=15000 / Error=0.0001 / #rare=3]

Initializing data structures:
  * Impute monomorphic [n=951] (0.00s)
  * HAP update (0.00s)
  * H2V transpose (0.00s)
  * PBWT parameters auto setting : [modulo = 0.039 / depth = 6]
  * PBWT initialization [#eval=22 / #select=1 / #chunk=1] (0.00s)
  * PBWT phasing sweep (0.01s)
  * Build genotype graphs [seg=2345] (0.00s)

Burn-in iteration [1/5]
  * PBWT selection (0.00s)
  * HMM computations [0%]
ERROR: Haploid underflow impossible to recover for [0_UMKLM_000010_s1]

I have checked the 0_UMKLM_000010_s1 sample. There is no missing genotype for this sample