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 21604168 on chromosome 'chr13' Hiding further warnings of this type, use --debug to show # Working on contig chr13 in individual FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1 Found 1721 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: 153922 Skipped 0 groups Found 661270 reads covering 1721 variants Kept 162441 reads that cover at least two variants each Selected 5548 most phase-informative reads covering 1035 variants Best-case phasing would result in 358 non-singleton phased blocks (0 singletons). Phasing 1 sample by solving the MEC problem ... Largest block contains 63 variants (6.1% of accessible variants) between position 25096120 and 25098167 # Working on contig chr13 in individual reference-NA12878 Found 48 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: 1.064 GB Time spent reading BAM/CRAM: 123.5 s Time spent parsing VCF: 0.1 s Time spent selecting reads: 9.1 s Time spent phasing: 3.2 s Time spent writing VCF: 0.1 s Time spent finding components: 0.0 s Time spent on rest: 1.1 s Total elapsed time: 137.1 s