This is WhatsHap 2.8 running under Python 3.9.23
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
[E::idx_find_and_load] Could not retrieve index file for 'input_filtered.vcf.gz'
[E::idx_find_and_load] Could not retrieve index file for 'input_filtered.vcf.gz'
[E::idx_find_and_load] Could not retrieve index file for 'input_filtered.vcf.gz'
Working on 2 samples from 2 families
WARNING: Skipping duplicated position 1016713 on chromosome 'chr11' Hiding further warnings of this type, use --debug to show

# Working on contig chr11 in individual NA12878_c_0002_gDNA_0001_B23KGCJLT4_1
Found 976 usable heterozygous variants (0 skipped due to missing genotypes)
[W::hts_idx_load3] The index file is older than the data file: NA12878_c_0002_gDNA_0001_B23KGCJLT4_1.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 55591
Skipped 0 groups
Found 188143 reads covering 976 variants
Kept 51392 reads that cover at least two variants each
Selected 1478 most phase-informative reads covering 633 variants
Best-case phasing would result in 77 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 237 variants (37.4% of accessible variants) between position 1016640 and 1018496

# Working on contig chr11 in individual reference-NA12878
Found 0 usable heterozygous variants (0 skipped due to missing genotypes)
WARNING: Sample 'reference-NA12878' not found in any BAM/CRAM file.
Found 0 reads covering 0 variants
Kept 0 reads that cover at least two variants each
Selected 0 most phase-informative reads covering 0 variants
Best-case phasing would result in 0 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
No. of phased blocks: 0
WARNING: Ignoring existing phasing information found in input VCF (PS tag exists).

# Resource usage
Maximum memory usage: 0.512 GB
Time spent reading BAM/CRAM:                  100.8 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     2.1 s
Time spent phasing:                             1.7 s
Time spent writing VCF:                         0.0 s
Time spent finding components:                  0.0 s
Time spent on rest:                             0.5 s
Total elapsed time:                           105.1 s