Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260504_LH00527_0080_B23VCL7LT4__c86dea0e--20260506-132014/alignments/recalibrated/1136_8DK-T1-TDNA-1_B23VCL7LT4_1/1136_8DK-T1-TDNA-1_B23VCL7LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/fa0d26aed41ab188837b6f9ca86c29/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/09cd493b6a496d6839caaef4160c70/1136_8DK-T1-TDNA-1_B23VCL7LT4_1_vs_1136_8DK-N1-BDNA-1_B23KFG5LT4_1.snv_indel.merged.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/fa0d26aed41ab188837b6f9ca86c29/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/09cd493b6a496d6839caaef4160c70/1136_8DK-T1-TDNA-1_B23VCL7LT4_1_vs_1136_8DK-N1-BDNA-1_B23KFG5LT4_1.snv_indel.merged.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260504_LH00527_0080_B23VCL7LT4__c86dea0e--20260506-132014/alignments/recalibrated/1136_8DK-T1-TDNA-1_B23VCL7LT4_1/1136_8DK-T1-TDNA-1_B23VCL7LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (8 inputs)

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 865494 on chromosome 'chr11' Hiding further warnings of this type, use --debug to show

# Working on contig chr11 in individual 1136_8DK-N1-BDNA-1_B23KFG5LT4_1
Found 173 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 chr11 in individual 1136_8DK-T1-TDNA-1_B23VCL7LT4_1
Found 1338 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: 123082
Skipped 0 groups
Found 288476 reads covering 1338 variants
Kept 59734 reads that cover at least two variants each
Selected 2379 most phase-informative reads covering 720 variants
Best-case phasing would result in 148 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 190 variants (26.4% of accessible variants) between position 1016640 and 1018523
WARNING: Ignoring existing phasing information found in input VCF (PS tag exists).

# Resource usage
Maximum memory usage: 0.512 GB
Time spent reading BAM/CRAM:                  212.0 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     2.4 s
Time spent phasing:                             1.9 s
Time spent writing VCF:                         0.0 s
Time spent finding components:                  0.0 s
Time spent on rest:                             0.5 s
Total elapsed time:                           217.0 s