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/34/bcf97783c5af44b1b63f02f00c2b06/.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/34/bcf97783c5af44b1b63f02f00c2b06/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/9b9bdd2e3a62b63766fd1bff60945d/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/6de69790aac1e89e822974adfc6541/negative_somatic_control_2.snv_indel.merged.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/9b9bdd2e3a62b63766fd1bff60945d/Sig_18_Blood.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/6de69790aac1e89e822974adfc6541/negative_somatic_control_2.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: Sig_18_Blood.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.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 41466166 on chromosome 'chr21' Hiding further warnings of this type, use --debug to show

# Working on contig chr21 in individual Sig_18_Blood
Found 166 usable heterozygous variants (0 skipped due to missing genotypes)
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 3814
Skipped 0 groups
Found 17162 reads covering 166 variants
Kept 2128 reads that cover at least two variants each
Selected 322 most phase-informative reads covering 63 variants
Best-case phasing would result in 23 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 5 variants (7.9% of accessible variants) between position 10413729 and 10413793

# Working on contig chr21 in individual reference-NA12878
Found 5 usable heterozygous variants (0 skipped due to missing genotypes)
WARNING: Sample 'reference-NA12878' 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
WARNING: Ignoring existing phasing information found in input VCF (PS tag exists).

# Resource usage
Maximum memory usage: 0.174 GB
Time spent reading BAM/CRAM:                   10.5 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     0.1 s
Time spent phasing:                             0.3 s
Time spent writing VCF:                         0.0 s
Time spent finding components:                  0.0 s
Time spent on rest:                             0.1 s
Total elapsed time:                            11.0 s