Minimac4 “Exec format error” when reading MSAV converted from 1000G m3vcf.gz

[Benyapa-ins]

Hi,
I am performing genotype imputation using:

• Phasing: EAGLE
• Imputation: Minimac4 v4.1.6 (Linux x86_64 binary)
• Reference panel: 1000G Phase 3 v5 (.m3vcf.gz)
• Running in All of Us research workbench Jupyter cloud workspace

Phasing completed successfully.

Issue: Exec Format Error with MSAV
Following the Minimac documentation, I attempted to convert the reference panel:

minimac4 --update-m3vcf chr15.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz > chr15.reference.msav

The conversion appeared to complete successfully. However, when using the generated .msav file:

[E::hts_hopen] Failed to open file chr15.reference.msav
[E::hts_open_format] Exec format error
Failed to read from chr15.reference.msav: Exec format error

Checking the file type:
file chr15.reference.msav
returns:
Zstandard compressed data (v0.8+)

Could you please help? Thank you.

Best,
Benyapa

[jonathonl]

[E::hts_hopen] Failed to open file chr15.reference.msav
[E::hts_open_format] Exec format error
Failed to read from chr15.reference.msav: Exec format error

Hi Benyapa,

Which tool is printing these error messages? These messages would not come from Minimac v4.1.6.