Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/4e6451c72168f432b05c97703f9143/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/4e6451c72168f432b05c97703f9143/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0069_A23KCGYLT4__d7a6b981--20260320-093016/alignments/recalibrated/1029_0W2-T1-TDNA-1_A23KCGYLT4_1/1029_0W2-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0069_A23KCGYLT4__d7a6b981--20260320-093016/alignments/recalibrated/1029_0W2-T1-TDNA-1_A23KCGYLT4_1/1029_0W2-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
  Downloading: s3://ai-pipelines-experiment/chnobles/ref_data/dbsnp138.snps.hg38.tsv.gz
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1029_0W2-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0W2-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Loaded 53092669 sites across 3366 contigs
Loaded 53092669 sites across 3366 contigs
Reads: 461015399 total, 3945421 skipped (flags/unmapped), 39905205 no site overlap
Fragments: 216631828 total (199423931 paired, 1909 singletons, 1109014 discordant, 16096974 orphans)
Sites: 53092669 total, 10156821 with data, 4335314 output (depth>=10)
Reads: 497007630 total, 3690467 skipped (flags/unmapped), 43203720 no site overlap
Fragments: 233331000 total (215644312 paired, 2178 singletons, 1138131 discordant, 16546379 orphans)
Sites: 53092669 total, 9488436 with data, 4118502 output (depth>=10)