This is WhatsHap 2.8 running under Python 3.9.23 [W::hts_idx_load3] The index file is older than the data file: 1029_01F-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_01F-T1-TDNA-1_A23TNVYLT4_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 10414738 on chromosome 'chr21' Hiding further warnings of this type, use --debug to show # Working on contig chr21 in individual 1029_01F-N1-BDNA-1_B23KFG5LT4_1 Found 0 usable heterozygous variants (0 skipped due to missing genotypes) WARNING: Sample '1029_01F-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 chr21 in individual 1029_01F-T1-TDNA-1_A23TNVYLT4_1 Found 234 usable heterozygous variants (0 skipped due to missing genotypes) [W::hts_idx_load3] The index file is older than the data file: 1029_01F-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam.bai Number of supplementary alignments: 0 Number of non-singleton groups: 16705 Skipped 0 groups Found 67455 reads covering 234 variants Kept 16891 reads that cover at least two variants each Selected 548 most phase-informative reads covering 124 variants Best-case phasing would result in 33 non-singleton phased blocks (0 singletons). Phasing 1 sample by solving the MEC problem ... Largest block contains 27 variants (21.8% of accessible variants) between position 44573789 and 44601223 WARNING: Ignoring existing phasing information found in input VCF (PS tag exists). # Resource usage Maximum memory usage: 0.177 GB Time spent reading BAM/CRAM: 38.3 s Time spent parsing VCF: 0.0 s Time spent selecting reads: 0.5 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: 39.3 s