[W::hts_idx_load3] The index file is older than the data file: custom_Sig_18_tumor_normal.snv_indel.merged.vcf.gz.tbi 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_tissue.recalibrated.bam.bai [W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.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 18294209 on chromosome 'chr21' Hiding further warnings of this type, use --debug to show # Working on contig chr21 in individual Sig_18_Blood Found 2 usable heterozygous variants (0 skipped due to missing genotypes) WARNING: Sample 'Sig_18_Blood' 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 Sig_18_tissue Found 231 usable heterozygous variants (0 skipped due to missing genotypes) [W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai Number of supplementary alignments: 0 Number of non-singleton groups: 53722 Skipped 0 groups Found 152557 reads covering 231 variants Kept 33869 reads that cover at least two variants each Selected 541 most phase-informative reads covering 100 variants Best-case phasing would result in 37 non-singleton phased blocks (0 singletons). Phasing 1 sample by solving the MEC problem ... Largest block contains 8 variants (8.0% of accessible variants) between position 10413729 and 10413840 WARNING: Ignoring existing phasing information found in input VCF (PS tag exists). # Resource usage Maximum memory usage: 0.308 GB Time spent reading BAM/CRAM: 96.3 s Time spent parsing VCF: 0.0 s Time spent selecting reads: 2.2 s Time spent phasing: 0.4 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: 99.2 s