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/ba/ac6caa255402145bc86e6d9993568a/1136_8DR-T1-TDNA-1_A23NMKMLT4_1_vs_1136_8DR-N1-BDNA-1_A23NLN3LT4_1.snv_indel.merged.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/1fcd475c2cc51bd2e5bbc122a223c7/.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/ba/ac6caa255402145bc86e6d9993568a/1136_8DR-T1-TDNA-1_A23NMKMLT4_1_vs_1136_8DR-N1-BDNA-1_A23NLN3LT4_1.snv_indel.merged.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/1fcd475c2cc51bd2e5bbc122a223c7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260330_LH00527_0071_A23NMKMLT4__0ce77ad5--20260401-094121/alignments/recalibrated/1136_8DR-T1-TDNA-1_A23NMKMLT4_1/1136_8DR-T1-TDNA-1_A23NMKMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260330_LH00527_0071_A23NMKMLT4__0ce77ad5--20260401-094121/alignments/recalibrated/1136_8DR-T1-TDNA-1_A23NMKMLT4_1/1136_8DR-T1-TDNA-1_A23NMKMLT4_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_8DR-T1-TDNA-1_A23NMKMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8DR-T1-TDNA-1_A23NMKMLT4_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 1224935 on chromosome 'chr19' Hiding further warnings of this type, use --debug to show

# Working on contig chr19 in individual 1136_8DR-N1-BDNA-1_A23NLN3LT4_1
Found 3 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 chr19 in individual 1136_8DR-T1-TDNA-1_A23NMKMLT4_1
Found 1358 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_A23NMKMLT4_1.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 100818
Skipped 0 groups
Found 322807 reads covering 1345 variants
Kept 107960 reads that cover at least two variants each
Selected 2765 most phase-informative reads covering 840 variants
Best-case phasing would result in 167 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 123 variants (14.6% of accessible variants) between position 54220882 and 54633185
WARNING: Ignoring existing phasing information found in input VCF (PS tag exists).

# Resource usage
Maximum memory usage: 0.565 GB
Time spent reading BAM/CRAM:                  172.3 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     4.6 s
Time spent phasing:                             2.2 s
Time spent writing VCF:                         0.0 s
Time spent finding components:                  0.0 s
Time spent on rest:                             0.7 s
Total elapsed time:                           179.8 s