This is WhatsHap 2.8 running under Python 3.9.23 [W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.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 41466166 on chromosome 'chr21' Hiding further warnings of this type, use --debug to show # Working on contig chr21 in individual Sig_18_Blood Found 166 usable heterozygous variants (0 skipped due to missing genotypes) [W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai Number of supplementary alignments: 0 Number of non-singleton groups: 3814 Skipped 0 groups Found 17162 reads covering 166 variants Kept 2128 reads that cover at least two variants each Selected 322 most phase-informative reads covering 63 variants Best-case phasing would result in 23 non-singleton phased blocks (0 singletons). Phasing 1 sample by solving the MEC problem ... Largest block contains 5 variants (7.9% of accessible variants) between position 10413729 and 10413793 # Working on contig chr21 in individual reference-NA12878 Found 5 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: 0.174 GB Time spent reading BAM/CRAM: 17.5 s Time spent parsing VCF: 0.0 s Time spent selecting reads: 0.2 s Time spent phasing: 0.5 s Time spent writing VCF: 0.0 s Time spent finding components: 0.0 s Time spent on rest: 0.2 s Total elapsed time: 18.3 s