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_8DK-T1-TDNA-1_B23VCL7LT4_1.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_8DK-T1-TDNA-1_B23VCL7LT4_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 33871031 on chromosome 'chr15' Hiding further warnings of this type, use --debug to show # Working on contig chr15 in individual 1136_8DK-N1-BDNA-1_B23KFG5LT4_1 Found 95 usable heterozygous variants (0 skipped due to missing genotypes) WARNING: Sample '1136_8DK-N1-BDNA-1_B23KFG5LT4_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 chr15 in individual 1136_8DK-T1-TDNA-1_B23VCL7LT4_1 Found 621 usable heterozygous variants (0 skipped due to missing genotypes) [W::hts_idx_load3] The index file is older than the data file: 1136_8DK-T1-TDNA-1_B23VCL7LT4_1.recalibrated.bam.bai Number of supplementary alignments: 0 Number of non-singleton groups: 77874 Skipped 0 groups Found 203733 reads covering 621 variants Kept 25509 reads that cover at least two variants each Selected 1187 most phase-informative reads covering 234 variants Best-case phasing would result in 82 non-singleton phased blocks (0 singletons). Phasing 1 sample by solving the MEC problem ... Largest block contains 11 variants (4.7% of accessible variants) between position 23439979 and 23441038 WARNING: Ignoring existing phasing information found in input VCF (PS tag exists). # Resource usage Maximum memory usage: 0.418 GB Time spent reading BAM/CRAM: 282.8 s Time spent parsing VCF: 0.0 s Time spent selecting reads: 2.2 s Time spent phasing: 1.0 s Time spent writing VCF: 0.0 s Time spent finding components: 0.0 s Time spent on rest: 0.3 s Total elapsed time: 286.4 s