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 5695565 on chromosome 'chr2' Hiding further warnings of this type, use --debug to show

# Working on contig chr2 in individual FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1
Found 7903 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: 946209
Skipped 0 groups
Found 3947068 reads covering 7903 variants
Kept 1040469 reads that cover at least two variants each
Selected 26306 most phase-informative reads covering 4900 variants
Best-case phasing would result in 1678 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 29 variants (0.6% of accessible variants) between position 5693636 and 5700669

# Working on contig chr2 in individual reference-NA12878
Found 180 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: 6.078 GB
Time spent reading BAM/CRAM:                  789.6 s
Time spent parsing VCF:                         0.2 s
Time spent selecting reads:                    95.0 s
Time spent phasing:                            20.1 s
Time spent writing VCF:                         0.4 s
Time spent finding components:                  0.1 s
Time spent on rest:                             6.4 s
Total elapsed time:                           911.9 s