This is WhatsHap 2.8 running under Python 3.9.23 [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.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 # Working on contig chr21 in individual HCC1395_BL Found 0 usable heterozygous variants (0 skipped due to missing genotypes) WARNING: Sample 'HCC1395_BL' 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 HCC1395_tumor Found 204 usable heterozygous variants (0 skipped due to missing genotypes) [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai Number of supplementary alignments: 0 Number of non-singleton groups: 12264 Skipped 0 groups Found 45727 reads covering 204 variants Kept 12991 reads that cover at least two variants each Selected 619 most phase-informative reads covering 121 variants Best-case phasing would result in 40 non-singleton phased blocks (0 singletons). Phasing 1 sample by solving the MEC problem ... Largest block contains 8 variants (6.6% of accessible variants) between position 44573789 and 44592359 WARNING: Ignoring existing phasing information found in input VCF (PS tag exists). # Resource usage Maximum memory usage: 0.161 GB Time spent reading BAM/CRAM: 35.2 s Time spent parsing VCF: 0.0 s Time spent selecting reads: 1.2 s Time spent phasing: 0.7 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: 37.3 s