What is the cause of the problem Assertion `rdp == (ind_number[file]*2 failed when using phase_common_static?

[thierrygrange]

Dear colleague

I have started a phasing project using 482 genomes and dividing the bcf by chromosomes using phase_common_static from shapeit 5 (Version : 5.1.1 / commit = 990ed0d / release = 2023-05-08) on a Ubuntu 22.04 server. The project stopped after about 15 minutes with the following message:
phase_common_static: src/utils/xcf.h:430: int32_t xcf_reader::readRecord(uint32_t, char**): Assertion `rdp == (ind_number[file]*2)' failed.
Abandon (core dumped)

I don't understand the meaning of the message and what I should modify to avoid it. Any clues?

Thanks

Thierry

The command I used was
END=19
for ((i=1;i<=END;i++)); do
BCF=Input_chr$i.bcf
OUT=Out_phased_chr$i.bcf
MAP=MySpecies_Chr$i.gmap.gz
phase_common_static --input ${BCF} --region $i --map ${MAP} --output ${OUT} --thread 8 --log Mylog_phased_chr$i.log
done

The full log info of one of the chromosome was:
[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 : 28/12/2024 - 22:40:53

Files:

• Input : [Inout_chr18.bcf]
• Genetic Map : [MySpecies_Chr18.gmap.gz]
• Output : [Out_phased_chr18.bcf]
• Output format : [bcf]
• Output LOG : [Mylog_phased_chr18.log]

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 (17.95s)
  • Variants [#sites=1592328 / region=18]
  • Samples [#target=482 / #reference=0]
    phase_common_static: src/utils/xcf.h:430: int32_t xcf_reader::readRecord(uint32_t, char**): Assertion `rdp == (ind_number[file]*2)' failed.
    Abandon (core dumped)