Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0069_A23KCGYLT4__d7a6b981--20260320-093016/alignments/recalibrated/1029_0I-T1-TDNA-1_A23KCGYLT4_1/1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/8f2f9c5f3114ad956872c267c2e495/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/8f2f9c5f3114ad956872c267c2e495/.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/20260318_LH00519_0069_A23KCGYLT4__d7a6b981--20260320-093016/alignments/recalibrated/1029_0I-T1-TDNA-1_A23KCGYLT4_1/1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_0I-T1-TDNA-1_A23KCGYLT4_1.recalibrated.bam.bai
Loaded 53092669 sites across 3366 contigs
Loaded 53092669 sites across 3366 contigs
Reads: 626284479 total, 982087 skipped (flags/unmapped), 51279937 no site overlap
Fragments: 302263433 total (271329719 paired, 2451 singletons, 429303 discordant, 30501960 orphans)
Sites: 53092669 total, 11027749 with data, 4848417 output (depth>=10)
Reads: 710055071 total, 1124924 skipped (flags/unmapped), 59707269 no site overlap
Fragments: 341189223 total (305021554 paired, 2946 singletons, 3012101 discordant, 33152622 orphans)
Sites: 53092669 total, 10378683 with data, 4652963 output (depth>=10)