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/a5/e3329e733a245f8e4eb56758a1a0c4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/206c01ca9552d4dd451be025e684a4/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/6f/3b8f493c4bbd324b6d78581c167e95/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/206c01ca9552d4dd451be025e684a4/positive_somatic_control_1.snv_indel.merged.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/e3329e733a245f8e4eb56758a1a0c4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/3b8f493c4bbd324b6d78581c167e95/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.recalibrated.bam.bai
==> 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: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_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 1395636 on chromosome 'chr4' Hiding further warnings of this type, use --debug to show

# Working on contig chr4 in individual FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1
Found 3972 usable heterozygous variants (0 skipped due to missing genotypes)
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.recalibrated.bam.bai
Number of supplementary alignments: 0
Number of non-singleton groups: 386295
Skipped 0 groups
Found 1570818 reads covering 3972 variants
Kept 385948 reads that cover at least two variants each
Selected 12871 most phase-informative reads covering 2278 variants
Best-case phasing would result in 823 non-singleton phased blocks (0 singletons). 
Phasing 1 sample by solving the MEC problem ...
Largest block contains 43 variants (1.9% of accessible variants) between position 87614483 and 87616623

# Working on contig chr4 in individual reference-NA12878
Found 100 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: 2.488 GB
Time spent reading BAM/CRAM:                  354.1 s
Time spent parsing VCF:                         0.1 s
Time spent selecting reads:                    31.7 s
Time spent phasing:                            10.0 s
Time spent writing VCF:                         0.2 s
Time spent finding components:                  0.0 s
Time spent on rest:                             2.6 s
Total elapsed time:                           398.8 s