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/b2/af0c565907198621c40991bd318828/HCC1395_tumor.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/3c9d0a66858c12471cb7356bb57dd3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/af0c565907198621c40991bd318828/HCC1395_tumor.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/b39a5f47abd0fee8fc82d74915e105/positive_somatic_control_1.snv_indel.merged.vcf.gz
  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/71/b39a5f47abd0fee8fc82d74915e105/positive_somatic_control_1.snv_indel.merged.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/3c9d0a66858c12471cb7356bb57dd3/.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: HCC1395_tumor.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.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 28966883 on chromosome 'chr21' Hiding further warnings of this type, use --debug to show

# Working on contig chr21 in individual HCC1395_tumor
Found 169 usable heterozygous variants (0 skipped due to missing genotypes)
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 3165
Skipped 0 groups
Found 13002 reads covering 169 variants
Kept 2200 reads that cover at least two variants each
Selected 356 most phase-informative reads covering 73 variants
Best-case phasing would result in 26 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 7 variants (9.6% of accessible variants) between position 10462806 and 10462873

# Working on contig chr21 in individual reference-NA12878
Found 8 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: 0.170 GB
Time spent reading BAM/CRAM:                    5.7 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     0.1 s
Time spent phasing:                             0.2 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:                             6.0 s