Error in margin phase :No valid VCF entries found!

[kch4221]

CONTIGS FOUND IN PEPPER VCF:
NGS_011
[05-24-2024 04:15:10] INFO: [4/9] RUNNING THE FOLLOWING COMMAND

time margin phase /home/zhou_yiwei/TMP/01.Script/Biosuite_Nanopore_analysis/1-5/NGS_011/sum.bam /home/zhou_yiwei/TMP/01.Script/Biosuite_Nanopore_analysis/1-5/NGS_011/NGS_011.fasta /home/zhou_yiwei/TMP/01.Script/Biosuite_Nanopore_analysis/1-5/pepper/intermediate_files/PEPPER_VARIANT_FULL.vcf.gz /opt/margin_dir/params/phase/allParams.haplotag.ont-r94g507.snp.json -t 8 -V -o /home/zhou_yiwei/TMP/01.Script/Biosuite_Nanopore_analysis/1-5/pepper/intermediate_files/PHASED.PEPPER_MARGIN 2>&1 | tee /home/zhou_yiwei/TMP/01.Script/Biosuite_Nanopore_analysis/1-5/pepper/logs/2_margin_haplotag.log;
samtools index -@8 /home/zhou_yiwei/TMP/01.Script/Biosuite_Nanopore_analysis/1-5/pepper/intermediate_files/PHASED.PEPPER_MARGIN.haplotagged.bam

Running OpenMP with 8 threads.

Parsing model parameters from file: /opt/margin_dir/params/phase/allParams.haplotag.ont-r94g507.snp.json
Parsed 8 total VCF entries from /home/zhou_yiwei/TMP/01.Script/Biosuite_Nanopore_analysis/1-5/pepper/intermediate_files/PEPPER_VARIANT_FULL.vcf.gz; kept 0 HETs, skipped 0 for region, 2 for not being PASS, 6 for being homozygous, 0 for being INDEL
No valid VCF entries found!

real 0m0.006s
user 0m0.001s
sys 0m0.007s
[E::hts_open_format] Failed to open file "/home/zhou_yiwei/TMP/01.Script/Biosuite_Nanopore_analysis/1-5/pepper/intermediate_files/PHASED.PEPPER_MARGIN.haplotagged.bam" : No such file or directory