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/23/3953409238089bc730214d32b79297/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/dad5d981709cf398a518d9512e55a1/positive_somatic_control_2.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/79/a954511b40e76d107ffbd247f3a138/Sig_18_tissue.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/dad5d981709cf398a518d9512e55a1/positive_somatic_control_2.snv_indel.merged.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/a954511b40e76d107ffbd247f3a138/Sig_18_tissue.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/3953409238089bc730214d32b79297/.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: 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

# Working on contig chr21 in individual Sig_18_tissue
Found 180 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: 5152
Skipped 0 groups
Found 15033 reads covering 180 variants
Kept 2905 reads that cover at least two variants each
Selected 334 most phase-informative reads covering 66 variants
Best-case phasing would result in 25 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 7 variants (10.6% of accessible variants) between position 10413733 and 10413840

# 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: 0.172 GB
Time spent reading BAM/CRAM:                   18.2 s
Time spent parsing VCF:                         0.0 s
Time spent selecting reads:                     0.3 s
Time spent phasing:                             0.5 s
Time spent writing VCF:                         0.0 s
Time spent finding components:                  0.0 s
Time spent on rest:                             0.2 s
Total elapsed time:                            19.3 s