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/a4/73c3e737c5458963417fdb65660b4a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/1d4ab20980f8d731eb1f1cf3684bf8/1029_01F-T1-TDNA-1_A23TNVYLT4_1_vs_1029_01F-N1-BDNA-1_B23KFG5LT4_1.snv_indel.merged.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/1d4ab20980f8d731eb1f1cf3684bf8/1029_01F-T1-TDNA-1_A23TNVYLT4_1_vs_1029_01F-N1-BDNA-1_B23KFG5LT4_1.snv_indel.merged.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260504_LH00527_0081_A23TNVYLT4__c86dea0e--20260506-131012/alignments/recalibrated/1029_01F-T1-TDNA-1_A23TNVYLT4_1/1029_01F-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260504_LH00527_0081_A23TNVYLT4__c86dea0e--20260506-131012/alignments/recalibrated/1029_01F-T1-TDNA-1_A23TNVYLT4_1/1029_01F-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/73c3e737c5458963417fdb65660b4a/.command.run
==> 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: 1029_01F-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_01F-T1-TDNA-1_A23TNVYLT4_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 17785889 on chromosome 'chr2' Hiding further warnings of this type, use --debug to show

# Working on contig chr2 in individual 1029_01F-N1-BDNA-1_B23KFG5LT4_1
Found 9 usable heterozygous variants (0 skipped due to missing genotypes)
WARNING: Sample '1029_01F-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 chr2 in individual 1029_01F-T1-TDNA-1_A23TNVYLT4_1
Found 1425 usable heterozygous variants (0 skipped due to missing genotypes)
[W::hts_idx_load3] The index file is older than the data file: 1029_01F-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 97523
Skipped 0 groups
Found 415678 reads covering 1424 variants
Kept 72342 reads that cover at least two variants each
Selected 2893 most phase-informative reads covering 615 variants
Best-case phasing would result in 194 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 19 variants (3.1% of accessible variants) between position 95891778 and 97204314
WARNING: Ignoring existing phasing information found in input VCF (PS tag exists).

# Resource usage
Maximum memory usage: 0.654 GB
Time spent reading BAM/CRAM:                  283.8 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     3.1 s
Time spent phasing:                             1.7 s
Time spent writing VCF:                         0.0 s
Time spent finding components:                  0.0 s
Time spent on rest:                             0.4 s
Total elapsed time:                           289.1 s