[W::hts_idx_load3] The index file is older than the data file: 1136_8DR-T1-TDNA-1_A23TNVHLT4_1_vs_1136_8DR-N1-BDNA-1_A23NLN3LT4_1.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: 1136_8DR-T1-TDNA-1_A23TNVHLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8DR-T1-TDNA-1_A23TNVHLT4_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 22943162 on chromosome 'chr15' Hiding further warnings of this type, use --debug to show

# Working on contig chr15 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 chr15 in individual 1136_8DR-T1-TDNA-1_A23TNVHLT4_1
Found 599 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_A23TNVHLT4_1.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 37577
Skipped 0 groups
Found 151320 reads covering 599 variants
Kept 24463 reads that cover at least two variants each
Selected 1257 most phase-informative reads covering 248 variants
Best-case phasing would result in 89 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 8 variants (3.2% of accessible variants) between position 92901721 and 92901795
WARNING: Ignoring existing phasing information found in input VCF (PS tag exists).

# Resource usage
Maximum memory usage: 0.316 GB
Time spent reading BAM/CRAM:                  165.9 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     1.0 s
Time spent phasing:                             0.6 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:                           167.7 s