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 254368 on chromosome 'chr18' Hiding further warnings of this type, use --debug to show # Working on contig chr18 in individual FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1 Found 1525 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: 144990 Skipped 0 groups Found 639936 reads covering 1525 variants Kept 152298 reads that cover at least two variants each Selected 5161 most phase-informative reads covering 901 variants Best-case phasing would result in 331 non-singleton phased blocks (0 singletons). Phasing 1 sample by solving the MEC problem ... Largest block contains 16 variants (1.8% of accessible variants) between position 9886570 and 9887684 # Working on contig chr18 in individual reference-NA12878 Found 46 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: 1.028 GB Time spent reading BAM/CRAM: 120.9 s Time spent parsing VCF: 0.0 s Time spent selecting reads: 8.0 s Time spent phasing: 2.8 s Time spent writing VCF: 0.1 s Time spent finding components: 0.0 s Time spent on rest: 0.8 s Total elapsed time: 132.8 s