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 717426 on chromosome 'chr16' Hiding further warnings of this type, use --debug to show # Working on contig chr16 in individual FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1 Found 4412 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: 579783 Skipped 0 groups Found 2432600 reads covering 4412 variants Kept 683511 reads that cover at least two variants each Selected 16127 most phase-informative reads covering 3020 variants Best-case phasing would result in 984 non-singleton phased blocks (0 singletons). Phasing 1 sample by solving the MEC problem ... Largest block contains 41 variants (1.4% of accessible variants) between position 1229091 and 1256985 # Working on contig chr16 in individual reference-NA12878 Found 108 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: 3.746 GB Time spent reading BAM/CRAM: 369.1 s Time spent parsing VCF: 0.1 s Time spent selecting reads: 47.0 s Time spent phasing: 9.4 s Time spent writing VCF: 0.2 s Time spent finding components: 0.1 s Time spent on rest: 3.5 s Total elapsed time: 429.4 s