This is WhatsHap 2.8 running under Python 3.9.23 [W::hts_idx_load3] The index file is older than the data file: 1136_8DR-T1-TDNA-1_A23NMKMLT4_1.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_8DR-T1-TDNA-1_A23NMKMLT4_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 290563 on chromosome 'chr20' Hiding further warnings of this type, use --debug to show # Working on contig chr20 in individual 1136_8DR-N1-BDNA-1_A23NLN3LT4_1 Found 0 usable heterozygous variants (0 skipped due to missing genotypes) WARNING: Sample '1136_8DR-N1-BDNA-1_A23NLN3LT4_1' 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 # Working on contig chr20 in individual 1136_8DR-T1-TDNA-1_A23NMKMLT4_1 Found 312 usable heterozygous variants (0 skipped due to missing genotypes) [W::hts_idx_load3] The index file is older than the data file: 1136_8DR-T1-TDNA-1_A23NMKMLT4_1.recalibrated.bam.bai Number of supplementary alignments: 0 Number of non-singleton groups: 38964 Skipped 0 groups Found 141346 reads covering 312 variants Kept 19323 reads that cover at least two variants each Selected 674 most phase-informative reads covering 120 variants Best-case phasing would result in 47 non-singleton phased blocks (0 singletons). Phasing 1 sample by solving the MEC problem ... Largest block contains 19 variants (15.8% of accessible variants) between position 1611474 and 1915413 WARNING: Ignoring existing phasing information found in input VCF (PS tag exists). # Resource usage Maximum memory usage: 0.215 GB Time spent reading BAM/CRAM: 96.5 s Time spent parsing VCF: 0.0 s Time spent selecting reads: 0.9 s Time spent phasing: 0.3 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: 97.8 s