No variants found during rerun

[dmjask]

Hi,
I have previously successfully used PEPPER-Margin-DeepVariant to obtain haplotagged reads (--only-haplotag flag) for a chromosome of interest. Recently I needed to repeat this for different chromosome, which yielded empty vcf; no candidates or variants found according to PEPPER.
To troubleshoot I repeated the haplotagging for the original chromosome, which also resulted in empty vcf and no candidates/variants.

[01-23-2025 09:23:48] INFO: STARTING CANDIDATE FINDING. [01-23-2025 09:23:49] INFO: FINISHED PROCESSING, TOTAL CANDIDATES FOUND: 0 [01-23-2025 09:23:49] INFO: FINISHED PROCESSING, TOTAL VARIANTS IN PEPPER: 0 [01-23-2025 09:23:49] INFO: FINISHED PROCESSING, TOTAL VARIANTS SELECTED FOR RE-GENOTYPING: 0 [01-23-2025 09:23:49] INFO: FINISHED PROCESSING, TOTAL SNP VARIANTS SELECTED FOR RE-GENOTYPING: 0 [01-23-2025 09:23:49] INFO: FINISHED PROCESSING, TOTAL INDEL VARIANTS SELECTED FOR RE-GENOTYPING: 0

`Running OpenMP with 64 threads.

Parsing model parameters from file: /opt/margin_dir/params/phase/allParams.haplotag.ont-r94g507.snp.json
Parsed 0 total VCF entries from input.vcf.gz; kept 0 HETs, skipped 0 for region, 0 for not being PASS, 0 for being homozygous, 0 for being INDEL
No valid VCF entries found!`

I am running the software within a conda env.

singularity exec $pepper_margin_deepvariant run_pepper_margin_deepvariant call_variant \ -b "$indir/${ID}_${CHR}_${START_POS}_${END_POS}.bam" \ -f "${REF}" \ -o "${outdir}" \ -p "${POUT}" \ -t 64 \ --ont_r9_guppy5_sup \ --only_haplotag \ -v "$ref":"$ref"

Any suggestion what may be causing this issue?

Thanks!