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 28926416 on chromosome 'chr2' Hiding further warnings of this type, use --debug to show

# Working on contig chr2 in individual NA12878_c_0002_gDNA_0001_B23KGCJLT4_1
Found 844 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: 61645
Skipped 0 groups
Found 244217 reads covering 844 variants
Kept 43243 reads that cover at least two variants each
Selected 1655 most phase-informative reads covering 339 variants
Best-case phasing would result in 112 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 49 variants (14.5% of accessible variants) between position 88859617 and 88886146

# Working on contig chr2 in individual reference-NA12878
Found 1 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: 0.739 GB
Time spent reading BAM/CRAM:                  157.0 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     1.6 s
Time spent phasing:                             0.9 s
Time spent writing VCF:                         0.0 s
Time spent finding components:                  0.0 s
Time spent on rest:                             0.3 s
Total elapsed time:                           159.8 s