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 19827553 on chromosome 'chr14' Hiding further warnings of this type, use --debug to show # Working on contig chr14 in individual FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1 Found 4710 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: 721371 Skipped 0 groups Found 2094738 reads covering 4710 variants Kept 922359 reads that cover at least two variants each Selected 12360 most phase-informative reads covering 3556 variants Best-case phasing would result in 693 non-singleton phased blocks (0 singletons). Phasing 1 sample by solving the MEC problem ... Largest block contains 989 variants (27.8% of accessible variants) between position 104941621 and 104954108 # Working on contig chr14 in individual reference-NA12878 Found 74 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: 3.479 GB Time spent reading BAM/CRAM: 308.9 s Time spent parsing VCF: 0.1 s Time spent selecting reads: 55.7 s Time spent phasing: 11.1 s Time spent writing VCF: 0.2 s Time spent finding components: 0.1 s Time spent on rest: 8.5 s Total elapsed time: 384.5 s