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 1257406 on chromosome 'chr1' Hiding further warnings of this type, use --debug to show # Working on contig chr1 in individual FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1 Found 10934 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: 1230070 Skipped 0 groups Found 4801231 reads covering 10934 variants Kept 1371608 reads that cover at least two variants each Selected 36401 most phase-informative reads covering 7325 variants Best-case phasing would result in 2266 non-singleton phased blocks (0 singletons). Phasing 1 sample by solving the MEC problem ... Largest block contains 256 variants (3.5% of accessible variants) between position 152213249 and 152221071 # Working on contig chr1 in individual reference-NA12878 Found 211 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: 7.409 GB Time spent reading BAM/CRAM: 962.5 s Time spent parsing VCF: 0.3 s Time spent selecting reads: 119.6 s Time spent phasing: 29.6 s Time spent writing VCF: 0.5 s Time spent finding components: 0.1 s Time spent on rest: 9.5 s Total elapsed time: 1122.2 s