This is WhatsHap 2.8 running under Python 3.9.23
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_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 138824 on chromosome 'chr17' Hiding further warnings of this type, use --debug to show

# Working on contig chr17 in individual FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1
Found 6240 usable heterozygous variants (0 skipped due to missing genotypes)
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 904033
Skipped 0 groups
Found 3852281 reads covering 6240 variants
Kept 1009883 reads that cover at least two variants each
Selected 22636 most phase-informative reads covering 4254 variants
Best-case phasing would result in 1408 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 41 variants (1.0% of accessible variants) between position 21415257 and 21416533

# Working on contig chr17 in individual reference-NA12878
Found 125 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: 5.923 GB
Time spent reading BAM/CRAM:                  585.0 s
Time spent parsing VCF:                         0.1 s
Time spent selecting reads:                    66.5 s
Time spent phasing:                            13.1 s
Time spent writing VCF:                         0.3 s
Time spent finding components:                  0.1 s
Time spent on rest:                             5.1 s
Total elapsed time:                           670.1 s