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/7d/08fe888d8884144d097192974cfdd9/.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/9f/262353cbd4618d6171bdb789c05fd9/1136_8DR-T1-TDNA-1_B23TTLKLT4_1_vs_1136_8DR-N1-BDNA-1_A23NLN3LT4_1.snv_indel.merged.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260511_LH00527_0084_B23TTLKLT4__8afaba2b--20260513-165040/alignments/recalibrated/1136_8DR-T1-TDNA-1_B23TTLKLT4_1/1136_8DR-T1-TDNA-1_B23TTLKLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260511_LH00527_0084_B23TTLKLT4__8afaba2b--20260513-165040/alignments/recalibrated/1136_8DR-T1-TDNA-1_B23TTLKLT4_1/1136_8DR-T1-TDNA-1_B23TTLKLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/08fe888d8884144d097192974cfdd9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/262353cbd4618d6171bdb789c05fd9/1136_8DR-T1-TDNA-1_B23TTLKLT4_1_vs_1136_8DR-N1-BDNA-1_A23NLN3LT4_1.snv_indel.merged.vcf.gz.tbi
==> 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_B23TTLKLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_8DR-T1-TDNA-1_B23TTLKLT4_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 7495459 on chromosome 'chr12' Hiding further warnings of this type, use --debug to show

# Working on contig chr12 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 chr12 in individual 1136_8DR-T1-TDNA-1_B23TTLKLT4_1
Found 1111 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_B23TTLKLT4_1.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 87579
Skipped 0 groups
Found 310726 reads covering 1111 variants
Kept 74168 reads that cover at least two variants each
Selected 2104 most phase-informative reads covering 581 variants
Best-case phasing would result in 127 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 105 variants (18.1% of accessible variants) between position 11030508 and 11134043
WARNING: Ignoring existing phasing information found in input VCF (PS tag exists).

# Resource usage
Maximum memory usage: 0.549 GB
Time spent reading BAM/CRAM:                  659.8 s
Time spent parsing VCF:                         0.1 s
Time spent selecting reads:                    10.2 s
Time spent phasing:                             4.6 s
Time spent writing VCF:                         0.1 s
Time spent finding components:                  0.0 s
Time spent on rest:                             1.4 s
Total elapsed time:                           676.2 s