Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_16G-N1-BDNA-1_B23KGCJLT4_1/1029_16G-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/2cfaf677072a0eb26c411b983b920c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/2cfaf677072a0eb26c411b983b920c/.command.run
  Downloading: s3://ai-pipelines-experiment/chnobles/ref_data/dbsnp138.snps.hg38.tsv.gz
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_16G-N1-BDNA-1_B23KGCJLT4_1/1029_16G-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1029_16G-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_16G-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
Loaded 53092669 sites across 3366 contigs
Loaded 53092669 sites across 3366 contigs
Reads: 191155821 total, 129312 skipped (flags/unmapped), 16003340 no site overlap
Fragments: 91832671 total (83127446 paired, 711 singletons, 63052 discordant, 8641462 orphans)
Sites: 53092669 total, 8027590 with data, 3296026 output (depth>=10)
Reads: 208760366 total, 145739 skipped (flags/unmapped), 18693842 no site overlap
Fragments: 99557111 total (90056899 paired, 886 singletons, 306775 discordant, 9192551 orphans)
Sites: 53092669 total, 7595779 with data, 3223767 output (depth>=10)