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/6a/eae3ebf55fdab7ff68342d2e9f623c/.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-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/067c152780d25a434fa8751c00dd01/custom_Sig_18_tumor_normal.snv_indel.merged.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_tissue/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/eae3ebf55fdab7ff68342d2e9f623c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/067c152780d25a434fa8751c00dd01/custom_Sig_18_tumor_normal.snv_indel.merged.vcf.gz
==> STAGING COMPLETE (8 inputs)

[W::hts_idx_load3] The index file is older than the data file: custom_Sig_18_tumor_normal.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: Sig_18_tissue.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.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 18294209 on chromosome 'chr21' Hiding further warnings of this type, use --debug to show

# Working on contig chr21 in individual Sig_18_Blood
Found 2 usable heterozygous variants (0 skipped due to missing genotypes)
WARNING: Sample 'Sig_18_Blood' 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 chr21 in individual Sig_18_tissue
Found 231 usable heterozygous variants (0 skipped due to missing genotypes)
[W::hts_idx_load3] The index file is older than the data file: Sig_18_tissue.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 53722
Skipped 0 groups
Found 152557 reads covering 231 variants
Kept 33869 reads that cover at least two variants each
Selected 541 most phase-informative reads covering 100 variants
Best-case phasing would result in 37 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 8 variants (8.0% of accessible variants) between position 10413729 and 10413840
WARNING: Ignoring existing phasing information found in input VCF (PS tag exists).

# Resource usage
Maximum memory usage: 0.308 GB
Time spent reading BAM/CRAM:                   96.3 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     2.2 s
Time spent phasing:                             0.4 s
Time spent writing VCF:                         0.0 s
Time spent finding components:                  0.0 s
Time spent on rest:                             0.3 s
Total elapsed time:                            99.2 s